Starting phenix.real_space_refine on Thu Dec 14 14:21:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ci0_2513/12_2023/4ci0_2513_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ci0_2513/12_2023/4ci0_2513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ci0_2513/12_2023/4ci0_2513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ci0_2513/12_2023/4ci0_2513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ci0_2513/12_2023/4ci0_2513_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ci0_2513/12_2023/4ci0_2513_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 216 7.16 5 Ni 12 6.56 5 Zn 12 6.06 5 P 24 5.49 5 S 864 5.16 5 C 52356 2.51 5 N 14136 2.21 5 O 15852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 248": "NH1" <-> "NH2" Residue "E ARG 248": "NH1" <-> "NH2" Residue "H ARG 248": "NH1" <-> "NH2" Residue "K ARG 248": "NH1" <-> "NH2" Residue "N ARG 248": "NH1" <-> "NH2" Residue "Q ARG 248": "NH1" <-> "NH2" Residue "T ARG 248": "NH1" <-> "NH2" Residue "W ARG 248": "NH1" <-> "NH2" Residue "Z ARG 248": "NH1" <-> "NH2" Residue "2 ARG 248": "NH1" <-> "NH2" Residue "5 ARG 248": "NH1" <-> "NH2" Residue "8 ARG 248": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 83472 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2985 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 359} Chain: "B" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "C" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2145 Classifications: {'peptide': 280} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 266} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 1, ' NI': 1, 'FE2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' ZN': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2985 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 359} Chain: "E" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "F" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2145 Classifications: {'peptide': 280} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 266} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 1, ' NI': 1, 'FE2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' ZN': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2985 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 359} Chain: "H" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "I" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2145 Classifications: {'peptide': 280} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 266} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 1, ' NI': 1, 'FE2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' ZN': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2985 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 359} Chain: "K" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "L" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2145 Classifications: {'peptide': 280} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 266} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 1, ' NI': 1, 'FE2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' ZN': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2985 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 359} Chain: "N" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "O" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2145 Classifications: {'peptide': 280} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 266} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 1, ' NI': 1, 'FE2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' ZN': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2985 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 359} Chain: "Q" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "R" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2145 Classifications: {'peptide': 280} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 266} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 1, ' NI': 1, 'FE2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' ZN': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2985 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 359} Chain: "T" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "U" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2145 Classifications: {'peptide': 280} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 266} Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 1, ' NI': 1, 'FE2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' ZN': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2985 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 359} Chain: "W" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "X" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2145 Classifications: {'peptide': 280} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 266} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 1, ' NI': 1, 'FE2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' ZN': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2985 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 359} Chain: "Z" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "0" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2145 Classifications: {'peptide': 280} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 266} Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 1, ' NI': 1, 'FE2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' ZN': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "0" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2985 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 359} Chain: "2" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "3" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2145 Classifications: {'peptide': 280} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 266} Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 1, ' NI': 1, 'FE2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' ZN': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "3" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2985 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 359} Chain: "5" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "6" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2145 Classifications: {'peptide': 280} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 266} Chain: "4" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 1, ' NI': 1, 'FE2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' ZN': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2985 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 359} Chain: "8" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "9" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2145 Classifications: {'peptide': 280} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 266} Chain: "7" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' FE': 1, ' NI': 1, 'FE2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "8" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' ZN': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "9" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'FAD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 493 SG CYS A 66 94.471 67.468 41.675 1.00 20.00 S ATOM 2962 SG CYS A 383 91.809 67.124 41.216 1.00 20.00 S ATOM 476 SG CYS A 63 93.981 64.698 40.205 1.00 20.00 S ATOM 493 SG CYS A 66 94.471 67.468 41.675 1.00 20.00 S ATOM 2942 SG CYS A 380 92.833 66.035 37.831 1.00 20.00 S ATOM 2962 SG CYS A 383 91.809 67.124 41.216 1.00 20.00 S ATOM 3078 SG CYS B 57 96.326 58.061 41.870 1.00 19.81 S ATOM 3660 SG CYS B 132 93.086 52.654 42.870 1.00 20.00 S ATOM 3946 SG CYS B 171 97.441 54.513 45.671 1.00 19.41 S ATOM 4518 SG CYS B 249 95.900 49.618 54.882 1.00 9.25 S ATOM 4541 SG CYS B 252 99.665 49.815 49.982 1.00 10.77 S ATOM 4369 SG CYS B 230 101.924 52.525 54.805 1.00 8.33 S ATOM 4559 SG CYS B 255 100.860 46.077 54.184 1.00 9.44 S ATOM 4310 SG CYS B 220 107.298 40.248 61.734 1.00 5.70 S ATOM 4328 SG CYS B 223 111.960 42.643 58.024 1.00 13.25 S ATOM 4593 SG CYS B 259 106.970 40.873 56.332 1.00 7.43 S ATOM 4345 SG CYS B 226 106.440 45.048 57.867 1.00 6.50 S ATOM 4210 SG CYS B 206 92.009 43.634 55.515 1.00 20.00 S ATOM 4220 SG CYS B 208 92.992 45.154 58.605 1.00 20.00 S ATOM 25078 SG CYS K 206 89.841 42.084 57.708 1.00 20.00 S ATOM 25088 SG CYS K 208 88.853 45.503 58.105 1.00 20.00 S ATOM 5491 SG CYS C 104 115.846 38.125 60.726 1.00 20.00 S ATOM 6222 SG CYS C 195 118.630 33.875 60.564 1.00 20.00 S ATOM 6199 SG CYS C 192 114.899 35.446 64.898 1.00 20.00 S ATOM 5734 SG CYS C 134 120.326 37.140 64.710 1.00 20.00 S ATOM 7449 SG CYS D 66 117.219 137.999 119.374 1.00 20.00 S ATOM 9918 SG CYS D 383 117.400 136.907 121.862 1.00 20.00 S ATOM 7432 SG CYS D 63 116.820 140.255 121.571 1.00 20.00 S ATOM 7449 SG CYS D 66 117.219 137.999 119.374 1.00 20.00 S ATOM 9898 SG CYS D 380 119.533 139.823 122.665 1.00 20.00 S ATOM 9918 SG CYS D 383 117.400 136.907 121.862 1.00 20.00 S ATOM 10034 SG CYS E 57 111.624 145.242 122.238 1.00 19.81 S ATOM 10616 SG CYS E 132 107.691 146.499 127.105 1.00 20.00 S ATOM 10902 SG CYS E 171 106.470 146.453 121.740 1.00 19.41 S ATOM 11474 SG CYS E 249 96.126 144.473 122.250 1.00 9.25 S ATOM 11497 SG CYS E 252 100.233 148.830 120.711 1.00 10.77 S ATOM 11325 SG CYS E 230 97.856 146.052 115.985 1.00 8.33 S ATOM 11515 SG CYS E 255 94.642 150.025 120.105 1.00 9.44 S ATOM 11266 SG CYS E 220 85.100 154.058 115.094 1.00 5.70 S ATOM 11284 SG CYS E 223 89.503 156.907 111.389 1.00 13.25 S ATOM 11549 SG CYS E 259 89.872 156.004 116.861 1.00 7.43 S ATOM 11301 SG CYS E 226 91.030 152.192 114.812 1.00 6.50 S ATOM 11166 SG CYS E 206 92.161 145.912 128.043 1.00 20.00 S ATOM 11176 SG CYS E 208 90.514 144.008 125.496 1.00 20.00 S ATOM 18122 SG CYS H 206 89.479 144.656 129.817 1.00 20.00 S ATOM 18132 SG CYS H 208 91.131 141.621 128.877 1.00 20.00 S ATOM 12447 SG CYS F 104 84.681 160.884 109.453 1.00 20.00 S ATOM 13178 SG CYS F 195 82.354 165.398 109.241 1.00 20.00 S ATOM 13155 SG CYS F 192 79.730 160.150 110.105 1.00 20.00 S ATOM 12690 SG CYS F 134 80.851 162.245 104.937 1.00 20.00 S ATOM 14405 SG CYS G 66 64.441 133.805 125.238 1.00 20.00 S ATOM 16874 SG CYS G 383 64.259 135.784 123.376 1.00 20.00 S ATOM 14388 SG CYS G 63 64.834 136.630 126.629 1.00 20.00 S ATOM 14405 SG CYS G 66 64.441 133.805 125.238 1.00 20.00 S ATOM 16854 SG CYS G 380 62.121 137.513 125.853 1.00 20.00 S ATOM 16874 SG CYS G 383 64.259 135.784 123.376 1.00 20.00 S ATOM 16990 SG CYS H 57 70.023 138.935 131.110 1.00 19.81 S ATOM 17572 SG CYS H 132 73.949 143.947 130.670 1.00 20.00 S ATOM 17858 SG CYS H 171 75.176 138.879 132.423 1.00 19.41 S ATOM 18430 SG CYS H 249 85.522 138.711 130.396 1.00 9.25 S ATOM 18453 SG CYS H 252 81.410 138.713 135.013 1.00 10.77 S ATOM 18281 SG CYS H 230 83.795 133.332 133.979 1.00 8.33 S ATOM 18471 SG CYS H 255 87.000 138.549 136.347 1.00 9.44 S ATOM 18222 SG CYS H 220 96.542 135.189 141.834 1.00 5.70 S ATOM 18240 SG CYS H 223 92.138 132.646 145.755 1.00 13.25 S ATOM 18505 SG CYS H 259 91.765 137.500 143.072 1.00 7.43 S ATOM 18257 SG CYS H 226 90.614 134.291 140.165 1.00 6.50 S ATOM 11166 SG CYS E 206 92.161 145.912 128.043 1.00 20.00 S ATOM 11176 SG CYS E 208 90.514 144.008 125.496 1.00 20.00 S ATOM 18122 SG CYS H 206 89.479 144.656 129.817 1.00 20.00 S ATOM 18132 SG CYS H 208 91.131 141.621 128.877 1.00 20.00 S ATOM 19403 SG CYS I 104 96.957 132.158 150.154 1.00 20.00 S ATOM 20134 SG CYS I 195 99.278 133.473 154.482 1.00 20.00 S ATOM 20111 SG CYS I 192 101.908 132.535 149.250 1.00 20.00 S ATOM 19646 SG CYS I 134 100.789 128.364 152.952 1.00 20.00 S ATOM 21361 SG CYS J 66 87.359 37.014 84.797 1.00 20.00 S ATOM 23830 SG CYS J 383 90.022 36.470 84.629 1.00 20.00 S ATOM 21344 SG CYS J 63 87.855 34.702 82.679 1.00 20.00 S ATOM 21361 SG CYS J 66 87.359 37.014 84.797 1.00 20.00 S ATOM 23810 SG CYS J 380 89.003 32.914 84.734 1.00 20.00 S ATOM 23830 SG CYS J 383 90.022 36.470 84.629 1.00 20.00 S ATOM 23946 SG CYS K 57 85.517 34.047 75.865 1.00 19.81 S ATOM 24528 SG CYS K 132 88.764 33.185 70.438 1.00 20.00 S ATOM 24814 SG CYS K 171 84.403 36.440 71.248 1.00 19.41 S ATOM 25386 SG CYS K 249 85.942 43.484 63.555 1.00 9.25 S ATOM 25409 SG CYS K 252 82.182 38.928 65.377 1.00 10.77 S ATOM 25237 SG CYS K 230 79.914 44.376 66.314 1.00 8.33 S ATOM 25427 SG CYS K 255 80.988 41.635 60.447 1.00 9.44 S ATOM 25178 SG CYS K 220 74.550 46.790 52.421 1.00 5.70 S ATOM 25196 SG CYS K 223 69.889 44.089 55.915 1.00 13.25 S ATOM 25461 SG CYS K 259 74.883 41.909 54.818 1.00 7.43 S ATOM 25213 SG CYS K 226 75.406 44.753 58.239 1.00 6.50 S ATOM 4210 SG CYS B 206 92.009 43.634 55.515 1.00 20.00 S ATOM 4220 SG CYS B 208 92.992 45.154 58.605 1.00 20.00 S ATOM 25078 SG CYS K 206 89.841 42.084 57.708 1.00 20.00 S ATOM 25088 SG CYS K 208 88.853 45.503 58.105 1.00 20.00 S ATOM 26359 SG CYS L 104 66.006 45.118 50.750 1.00 20.00 S ATOM 27090 SG CYS L 195 63.228 43.539 46.796 1.00 20.00 S ATOM 27067 SG CYS L 192 66.953 48.154 46.830 1.00 20.00 S ATOM 26602 SG CYS L 134 61.524 48.537 48.484 1.00 20.00 S ATOM 28317 SG CYS M 66 66.044 104.191 41.657 1.00 20.00 S ATOM 30786 SG CYS M 383 67.077 106.668 41.195 1.00 20.00 S ATOM 28300 SG CYS M 63 63.890 105.999 40.185 1.00 20.00 S ATOM 28317 SG CYS M 66 66.044 104.191 41.657 1.00 20.00 S ATOM 30766 SG CYS M 380 65.623 106.321 37.810 1.00 20.00 S ATOM 30786 SG CYS M 383 67.077 106.668 41.195 1.00 20.00 S ATOM 30902 SG CYS N 57 56.970 107.288 41.847 1.00 19.81 S ATOM 31484 SG CYS N 132 53.907 112.799 42.839 1.00 20.00 S ATOM 31770 SG CYS N 171 53.339 108.102 45.646 1.00 19.41 S ATOM 32342 SG CYS N 249 49.868 111.896 54.851 1.00 9.25 S ATOM 32365 SG CYS N 252 48.157 108.530 49.955 1.00 10.77 S ATOM 32193 SG CYS N 230 49.374 105.225 54.783 1.00 8.33 S ATOM 32383 SG CYS N 255 44.322 109.370 54.155 1.00 9.44 S ATOM 32134 SG CYS N 220 36.053 106.718 61.707 1.00 5.70 S ATOM 32152 SG CYS N 223 35.797 101.479 58.004 1.00 13.25 S ATOM 32417 SG CYS N 259 36.760 106.683 56.305 1.00 7.43 S ATOM 32169 SG CYS N 226 40.640 105.056 57.843 1.00 6.50 S ATOM 32034 SG CYS N 206 46.631 118.258 55.476 1.00 20.00 S ATOM 32044 SG CYS N 208 47.456 116.651 58.568 1.00 20.00 S ATOM 52902 SG CYS W 206 46.372 120.914 57.665 1.00 20.00 S ATOM 52912 SG CYS W 208 49.827 120.060 58.064 1.00 20.00 S ATOM 33315 SG CYS O 104 29.941 100.376 60.706 1.00 20.00 S ATOM 34046 SG CYS O 195 24.868 100.090 60.544 1.00 20.00 S ATOM 34023 SG CYS O 192 28.094 102.541 64.875 1.00 20.00 S ATOM 33558 SG CYS O 134 26.847 96.994 64.694 1.00 20.00 S ATOM 35273 SG CYS P 66 115.737 49.325 119.436 1.00 20.00 S ATOM 37742 SG CYS P 383 114.700 49.717 121.923 1.00 20.00 S ATOM 35256 SG CYS P 63 117.889 48.545 121.634 1.00 20.00 S ATOM 35273 SG CYS P 66 115.737 49.325 119.436 1.00 20.00 S ATOM 37722 SG CYS P 380 116.159 46.414 122.731 1.00 20.00 S ATOM 37742 SG CYS P 383 114.700 49.717 121.923 1.00 20.00 S ATOM 37858 SG CYS Q 57 124.806 50.552 122.300 1.00 19.81 S ATOM 38440 SG CYS Q 132 127.861 53.336 127.164 1.00 20.00 S ATOM 38726 SG CYS Q 171 128.432 54.410 121.798 1.00 19.41 S ATOM 39298 SG CYS Q 249 131.889 64.359 122.296 1.00 9.25 S ATOM 39321 SG CYS Q 252 133.609 58.621 120.765 1.00 10.77 S ATOM 39149 SG CYS Q 230 132.392 62.063 116.034 1.00 8.33 S ATOM 39339 SG CYS Q 255 137.439 62.865 120.154 1.00 9.44 S ATOM 39090 SG CYS Q 220 145.704 69.106 115.137 1.00 5.70 S ATOM 39108 SG CYS Q 223 145.971 63.863 111.439 1.00 13.25 S ATOM 39373 SG CYS Q 259 145.003 64.003 116.910 1.00 7.43 S ATOM 39125 SG CYS Q 226 141.124 64.902 114.859 1.00 6.50 S ATOM 38990 SG CYS Q 206 135.116 67.081 128.086 1.00 20.00 S ATOM 39000 SG CYS Q 208 134.291 69.456 125.536 1.00 20.00 S ATOM 45946 SG CYS T 206 135.370 70.033 129.857 1.00 20.00 S ATOM 45956 SG CYS T 208 131.915 70.119 128.915 1.00 20.00 S ATOM 40271 SG CYS R 104 151.826 66.048 109.501 1.00 20.00 S ATOM 41002 SG CYS R 195 156.899 65.806 109.290 1.00 20.00 S ATOM 40979 SG CYS R 192 153.667 70.704 110.147 1.00 20.00 S ATOM 40514 SG CYS R 134 154.921 68.679 104.982 1.00 20.00 S ATOM 42229 SG CYS S 66 138.492 97.137 125.243 1.00 20.00 S ATOM 44698 SG CYS S 383 140.298 96.302 123.383 1.00 20.00 S ATOM 42212 SG CYS S 63 140.742 95.385 126.637 1.00 20.00 S ATOM 42229 SG CYS S 66 138.492 97.137 125.243 1.00 20.00 S ATOM 44678 SG CYS S 380 142.864 97.292 125.859 1.00 20.00 S ATOM 44698 SG CYS S 383 140.298 96.302 123.383 1.00 20.00 S ATOM 44814 SG CYS T 57 140.143 89.745 131.125 1.00 19.81 S ATOM 45396 SG CYS T 132 142.521 83.838 130.693 1.00 20.00 S ATOM 45682 SG CYS T 171 137.518 85.312 132.443 1.00 19.41 S ATOM 46254 SG CYS T 249 132.199 76.434 130.426 1.00 9.25 S ATOM 46277 SG CYS T 252 134.256 79.999 135.039 1.00 10.77 S ATOM 46105 SG CYS T 230 128.404 80.623 134.004 1.00 8.33 S ATOM 46295 SG CYS T 255 131.319 75.242 136.379 1.00 9.44 S ATOM 46046 SG CYS T 220 123.638 68.665 141.873 1.00 5.70 S ATOM 46064 SG CYS T 223 123.636 73.756 145.787 1.00 13.25 S ATOM 46329 SG CYS T 259 128.026 71.648 143.107 1.00 7.43 S ATOM 46081 SG CYS T 226 125.824 74.246 140.197 1.00 6.50 S ATOM 38990 SG CYS Q 206 135.116 67.081 128.086 1.00 20.00 S ATOM 39000 SG CYS Q 208 134.291 69.456 125.536 1.00 20.00 S ATOM 45946 SG CYS T 206 135.370 70.033 129.857 1.00 20.00 S ATOM 45956 SG CYS T 208 131.915 70.119 128.915 1.00 20.00 S ATOM 47227 SG CYS U 104 120.804 69.832 150.191 1.00 20.00 S ATOM 47958 SG CYS U 195 120.781 67.170 154.522 1.00 20.00 S ATOM 47935 SG CYS U 192 118.654 65.355 149.292 1.00 20.00 S ATOM 47470 SG CYS U 134 115.601 68.414 152.990 1.00 20.00 S ATOM 49185 SG CYS V 66 43.217 125.632 84.747 1.00 20.00 S ATOM 51654 SG CYS V 383 41.415 123.598 84.581 1.00 20.00 S ATOM 49168 SG CYS V 63 40.968 126.356 82.628 1.00 20.00 S ATOM 49185 SG CYS V 66 43.217 125.632 84.747 1.00 20.00 S ATOM 51634 SG CYS V 380 38.845 126.258 84.683 1.00 20.00 S ATOM 51654 SG CYS V 383 41.415 123.598 84.581 1.00 20.00 S ATOM 51770 SG CYS W 57 41.571 128.700 75.811 1.00 19.81 S ATOM 52352 SG CYS W 132 39.202 126.312 70.387 1.00 20.00 S ATOM 52638 SG CYS W 171 44.201 128.462 71.195 1.00 19.41 S ATOM 53210 SG CYS W 249 49.534 123.597 63.509 1.00 9.25 S ATOM 53233 SG CYS W 252 47.467 129.135 65.323 1.00 10.77 S ATOM 53061 SG CYS W 230 53.319 128.375 66.263 1.00 8.33 S ATOM 53251 SG CYS W 255 50.410 128.809 60.394 1.00 9.44 S ATOM 53002 SG CYS W 220 58.095 131.796 52.366 1.00 5.70 S ATOM 53020 SG CYS W 223 58.086 137.188 55.854 1.00 13.25 S ATOM 53285 SG CYS W 259 53.701 133.951 54.760 1.00 7.43 S ATOM 53037 SG CYS W 226 55.902 132.081 58.184 1.00 6.50 S ATOM 32034 SG CYS N 206 46.631 118.258 55.476 1.00 20.00 S ATOM 32044 SG CYS N 208 47.456 116.651 58.568 1.00 20.00 S ATOM 52902 SG CYS W 206 46.372 120.914 57.665 1.00 20.00 S ATOM 52912 SG CYS W 208 49.827 120.060 58.064 1.00 20.00 S ATOM 54183 SG CYS X 104 60.919 140.029 50.685 1.00 20.00 S ATOM 54914 SG CYS X 195 60.941 143.219 46.727 1.00 20.00 S ATOM 54891 SG CYS X 192 63.076 137.686 46.769 1.00 20.00 S ATOM 54426 SG CYS X 134 66.121 142.199 48.417 1.00 20.00 S ATOM 56141 SG CYS Y 66 112.061 110.448 41.640 1.00 20.00 S ATOM 58610 SG CYS Y 383 113.689 108.314 41.181 1.00 20.00 S ATOM 56124 SG CYS Y 63 114.703 111.408 40.167 1.00 20.00 S ATOM 56141 SG CYS Y 66 112.061 110.448 41.640 1.00 20.00 S ATOM 58590 SG CYS Y 380 114.117 109.743 37.795 1.00 20.00 S ATOM 58610 SG CYS Y 383 113.689 108.314 41.181 1.00 20.00 S ATOM 58726 SG CYS Z 57 119.280 116.758 41.823 1.00 19.81 S ATOM 59308 SG CYS Z 132 125.584 116.657 42.817 1.00 20.00 S ATOM 59594 SG CYS Z 171 121.799 119.501 45.619 1.00 19.41 S ATOM 60166 SG CYS Z 249 126.818 120.621 54.824 1.00 9.25 S ATOM 60189 SG CYS Z 252 124.760 123.780 49.924 1.00 10.77 S ATOM 60017 SG CYS Z 230 121.288 124.385 54.750 1.00 8.33 S ATOM 60207 SG CYS Z 255 127.404 126.687 54.121 1.00 9.44 S ATOM 59958 SG CYS Z 220 129.241 135.183 61.662 1.00 5.70 S ATOM 59976 SG CYS Z 223 124.832 138.020 57.954 1.00 13.25 S ATOM 60241 SG CYS Z 259 128.858 134.582 56.261 1.00 7.43 S ATOM 59993 SG CYS Z 226 125.509 132.037 57.801 1.00 6.50 S ATOM 59858 SG CYS Z 206 133.947 120.244 55.450 1.00 20.00 S ATOM 59868 SG CYS Z 208 132.142 120.338 58.542 1.00 20.00 S ATOM 80726 SG CYS 8 206 136.376 119.143 57.641 1.00 20.00 S ATOM 80736 SG CYS 8 208 133.909 116.578 58.043 1.00 20.00 S ATOM 61139 SG CYS 0 104 126.804 143.646 60.650 1.00 20.00 S ATOM 61870 SG CYS 0 195 129.093 148.182 60.482 1.00 20.00 S ATOM 61847 SG CYS 0 192 129.602 144.169 64.818 1.00 20.00 S ATOM 61382 SG CYS 0 134 125.421 148.022 64.632 1.00 20.00 S ATOM 63097 SG CYS 1 66 39.684 94.946 119.425 1.00 20.00 S ATOM 65566 SG CYS 1 383 40.541 95.650 121.912 1.00 20.00 S ATOM 63080 SG CYS 1 63 37.932 93.474 121.625 1.00 20.00 S ATOM 63097 SG CYS 1 66 39.684 94.946 119.425 1.00 20.00 S ATOM 65546 SG CYS 1 380 36.951 96.040 122.718 1.00 20.00 S ATOM 65566 SG CYS 1 383 40.541 95.650 121.912 1.00 20.00 S ATOM 65682 SG CYS 2 57 36.211 86.481 122.299 1.00 19.81 S ATOM 66264 SG CYS 2 132 37.094 82.450 127.168 1.00 20.00 S ATOM 66550 SG CYS 2 171 37.739 81.411 121.804 1.00 19.41 S ATOM 67122 SG CYS 2 249 44.627 73.444 122.314 1.00 9.25 S ATOM 67145 SG CYS 2 252 38.798 74.821 120.780 1.00 10.77 S ATOM 66973 SG CYS 2 230 42.388 74.148 116.050 1.00 8.33 S ATOM 67163 SG CYS 2 255 40.559 69.381 120.176 1.00 9.44 S ATOM 66914 SG CYS 2 220 41.832 59.097 115.172 1.00 5.70 S ATOM 66932 SG CYS 2 223 37.158 61.483 111.470 1.00 13.25 S ATOM 67197 SG CYS 2 259 37.762 62.258 116.941 1.00 7.43 S ATOM 66949 SG CYS 2 226 40.482 65.165 114.887 1.00 6.50 S ATOM 66814 SG CYS 2 206 45.369 69.295 128.109 1.00 20.00 S ATOM 66824 SG CYS 2 208 47.839 68.819 125.560 1.00 20.00 S ATOM 73770 SG CYS 5 206 47.799 67.602 129.882 1.00 20.00 S ATOM 73780 SG CYS 5 208 49.600 70.550 128.938 1.00 20.00 S ATOM 68095 SG CYS 3 104 36.124 55.317 109.540 1.00 20.00 S ATOM 68826 SG CYS 3 195 33.378 51.044 109.334 1.00 20.00 S ATOM 68803 SG CYS 3 192 39.235 51.396 110.192 1.00 20.00 S ATOM 68338 SG CYS 3 134 36.855 51.316 105.026 1.00 20.00 S ATOM 70053 SG CYS 4 66 69.711 51.340 125.293 1.00 20.00 S ATOM 72522 SG CYS 4 383 68.086 50.192 123.435 1.00 20.00 S ATOM 70036 SG CYS 4 63 67.069 50.269 126.688 1.00 20.00 S ATOM 70053 SG CYS 4 66 69.711 51.340 125.293 1.00 20.00 S ATOM 72502 SG CYS 4 380 67.660 47.478 125.914 1.00 20.00 S ATOM 72522 SG CYS 4 383 68.086 50.192 123.435 1.00 20.00 S ATOM 72638 SG CYS 5 57 62.483 53.614 131.172 1.00 19.81 S ATOM 73220 SG CYS 5 132 56.179 54.508 130.737 1.00 20.00 S ATOM 73506 SG CYS 5 171 59.957 58.106 132.483 1.00 19.41 S ATOM 74078 SG CYS 5 249 54.927 67.148 130.454 1.00 9.25 S ATOM 74101 SG CYS 5 252 56.986 63.590 135.072 1.00 10.77 S ATOM 73929 SG CYS 5 230 60.452 68.345 134.031 1.00 8.33 S ATOM 74119 SG CYS 5 255 54.334 68.514 136.405 1.00 9.44 S ATOM 73870 SG CYS 5 220 52.478 78.461 141.885 1.00 5.70 S ATOM 73888 SG CYS 5 223 56.887 75.923 145.804 1.00 13.25 S ATOM 74153 SG CYS 5 259 52.867 73.171 143.127 1.00 7.43 S ATOM 73905 SG CYS 5 226 56.218 73.776 140.216 1.00 6.50 S ATOM 66814 SG CYS 2 206 45.369 69.295 128.109 1.00 20.00 S ATOM 66824 SG CYS 2 208 47.839 68.819 125.560 1.00 20.00 S ATOM 73770 SG CYS 5 206 47.799 67.602 129.882 1.00 20.00 S ATOM 73780 SG CYS 5 208 49.600 70.550 128.938 1.00 20.00 S ATOM 75051 SG CYS 6 104 54.904 80.343 150.202 1.00 20.00 S ATOM 75782 SG CYS 6 195 52.610 81.700 154.530 1.00 20.00 S ATOM 75759 SG CYS 6 192 52.102 84.443 149.297 1.00 20.00 S ATOM 75294 SG CYS 6 134 56.277 85.561 152.994 1.00 20.00 S ATOM 77009 SG CYS 7 66 142.034 119.551 84.724 1.00 20.00 S ATOM 79478 SG CYS 7 383 141.173 122.129 84.555 1.00 20.00 S ATOM 76992 SG CYS 7 63 143.786 121.134 82.603 1.00 20.00 S ATOM 77009 SG CYS 7 66 142.034 119.551 84.724 1.00 20.00 S ATOM 79458 SG CYS 7 380 144.762 123.024 84.656 1.00 20.00 S ATOM 79478 SG CYS 7 383 141.173 122.129 84.555 1.00 20.00 S ATOM 79594 SG CYS 8 57 145.515 119.432 75.789 1.00 19.81 S ATOM 80176 SG CYS 8 132 144.634 122.670 70.361 1.00 20.00 S ATOM 80462 SG CYS 8 171 143.995 117.267 71.176 1.00 19.41 S ATOM 81034 SG CYS 8 249 137.118 115.071 63.491 1.00 9.25 S ATOM 81057 SG CYS 8 252 142.946 114.095 65.308 1.00 10.77 S ATOM 80885 SG CYS 8 230 139.362 109.407 66.253 1.00 8.33 S ATOM 81075 SG CYS 8 255 141.194 111.703 60.382 1.00 9.44 S ATOM 80826 SG CYS 8 220 139.939 103.544 52.364 1.00 5.70 S ATOM 80844 SG CYS 8 223 144.613 100.860 55.855 1.00 13.25 S ATOM 81109 SG CYS 8 259 144.003 106.274 54.754 1.00 7.43 S ATOM 80861 SG CYS 8 226 141.282 105.308 58.179 1.00 6.50 S ATOM 59858 SG CYS Z 206 133.947 120.244 55.450 1.00 20.00 S ATOM 59868 SG CYS Z 208 132.142 120.338 58.542 1.00 20.00 S ATOM 80726 SG CYS 8 206 136.376 119.143 57.641 1.00 20.00 S ATOM 80736 SG CYS 8 208 133.909 116.578 58.043 1.00 20.00 S ATOM 82007 SG CYS 9 104 145.658 96.979 50.692 1.00 20.00 S ATOM 82738 SG CYS 9 195 148.410 95.360 46.737 1.00 20.00 S ATOM 82715 SG CYS 9 192 142.551 96.278 46.776 1.00 20.00 S ATOM 82250 SG CYS 9 134 144.936 91.386 48.431 1.00 20.00 S Time building chain proxies: 33.10, per 1000 atoms: 0.40 Number of scatterers: 83472 At special positions: 0 Unit cell: (183.48, 190.08, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 12 29.99 Ni 12 28.00 Fe 216 26.01 S 864 16.00 P 24 15.00 O 15852 8.00 N 14136 7.00 C 52356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.23 Conformation dependent library (CDL) restraints added in 11.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 01282 " pdb="FE1 SF4 01282 " - pdb=" SG CYS 0 104 " pdb="FE4 SF4 01282 " - pdb=" SG CYS 0 134 " pdb="FE3 SF4 01282 " - pdb=" SG CYS 0 192 " pdb="FE2 SF4 01282 " - pdb=" SG CYS 0 195 " pdb=" SF4 21274 " pdb="FE1 SF4 21274 " - pdb=" SG CYS 2 57 " pdb="FE2 SF4 21274 " - pdb=" SG CYS 2 132 " pdb="FE3 SF4 21274 " - pdb=" SG CYS 2 171 " pdb=" SF4 21275 " pdb="FE2 SF4 21275 " - pdb=" SG CYS 2 252 " pdb="FE1 SF4 21275 " - pdb=" SG CYS 2 249 " pdb="FE3 SF4 21275 " - pdb=" SG CYS 2 230 " pdb="FE4 SF4 21275 " - pdb=" SG CYS 2 255 " pdb=" SF4 21276 " pdb="FE3 SF4 21276 " - pdb=" SG CYS 2 259 " pdb="FE4 SF4 21276 " - pdb=" SG CYS 2 226 " pdb="FE1 SF4 21276 " - pdb=" SG CYS 2 220 " pdb="FE2 SF4 21276 " - pdb=" SG CYS 2 223 " pdb=" SF4 31282 " pdb="FE1 SF4 31282 " - pdb=" SG CYS 3 104 " pdb="FE4 SF4 31282 " - pdb=" SG CYS 3 134 " pdb="FE3 SF4 31282 " - pdb=" SG CYS 3 192 " pdb="FE2 SF4 31282 " - pdb=" SG CYS 3 195 " pdb=" SF4 51274 " pdb="FE1 SF4 51274 " - pdb=" SG CYS 5 57 " pdb="FE2 SF4 51274 " - pdb=" SG CYS 5 132 " pdb="FE3 SF4 51274 " - pdb=" SG CYS 5 171 " pdb=" SF4 51275 " pdb="FE2 SF4 51275 " - pdb=" SG CYS 5 252 " pdb="FE1 SF4 51275 " - pdb=" SG CYS 5 249 " pdb="FE3 SF4 51275 " - pdb=" SG CYS 5 230 " pdb="FE4 SF4 51275 " - pdb=" SG CYS 5 255 " pdb=" SF4 51276 " pdb="FE3 SF4 51276 " - pdb=" SG CYS 5 259 " pdb="FE4 SF4 51276 " - pdb=" SG CYS 5 226 " pdb="FE1 SF4 51276 " - pdb=" SG CYS 5 220 " pdb="FE2 SF4 51276 " - pdb=" SG CYS 5 223 " pdb=" SF4 61282 " pdb="FE1 SF4 61282 " - pdb=" SG CYS 6 104 " pdb="FE4 SF4 61282 " - pdb=" SG CYS 6 134 " pdb="FE3 SF4 61282 " - pdb=" SG CYS 6 192 " pdb="FE2 SF4 61282 " - pdb=" SG CYS 6 195 " pdb=" SF4 81274 " pdb="FE1 SF4 81274 " - pdb=" SG CYS 8 57 " pdb="FE2 SF4 81274 " - pdb=" SG CYS 8 132 " pdb="FE3 SF4 81274 " - pdb=" SG CYS 8 171 " pdb=" SF4 81275 " pdb="FE2 SF4 81275 " - pdb=" SG CYS 8 252 " pdb="FE1 SF4 81275 " - pdb=" SG CYS 8 249 " pdb="FE3 SF4 81275 " - pdb=" SG CYS 8 230 " pdb="FE4 SF4 81275 " - pdb=" SG CYS 8 255 " pdb=" SF4 81276 " pdb="FE3 SF4 81276 " - pdb=" SG CYS 8 259 " pdb="FE4 SF4 81276 " - pdb=" SG CYS 8 226 " pdb="FE1 SF4 81276 " - pdb=" SG CYS 8 220 " pdb="FE2 SF4 81276 " - pdb=" SG CYS 8 223 " pdb=" SF4 91282 " pdb="FE1 SF4 91282 " - pdb=" SG CYS 9 104 " pdb="FE4 SF4 91282 " - pdb=" SG CYS 9 134 " pdb="FE3 SF4 91282 " - pdb=" SG CYS 9 192 " pdb="FE2 SF4 91282 " - pdb=" SG CYS 9 195 " pdb=" SF4 B1274 " pdb="FE1 SF4 B1274 " - pdb=" SG CYS B 57 " pdb="FE2 SF4 B1274 " - pdb=" SG CYS B 132 " pdb="FE3 SF4 B1274 " - pdb=" SG CYS B 171 " pdb=" SF4 B1275 " pdb="FE2 SF4 B1275 " - pdb=" SG CYS B 252 " pdb="FE1 SF4 B1275 " - pdb=" SG CYS B 249 " pdb="FE3 SF4 B1275 " - pdb=" SG CYS B 230 " pdb="FE4 SF4 B1275 " - pdb=" SG CYS B 255 " pdb=" SF4 B1276 " pdb="FE3 SF4 B1276 " - pdb=" SG CYS B 259 " pdb="FE4 SF4 B1276 " - pdb=" SG CYS B 226 " pdb="FE1 SF4 B1276 " - pdb=" SG CYS B 220 " pdb="FE2 SF4 B1276 " - pdb=" SG CYS B 223 " pdb=" SF4 C1282 " pdb="FE1 SF4 C1282 " - pdb=" SG CYS C 104 " pdb="FE4 SF4 C1282 " - pdb=" SG CYS C 134 " pdb="FE3 SF4 C1282 " - pdb=" SG CYS C 192 " pdb="FE2 SF4 C1282 " - pdb=" SG CYS C 195 " pdb=" SF4 E1274 " pdb="FE1 SF4 E1274 " - pdb=" SG CYS E 57 " pdb="FE2 SF4 E1274 " - pdb=" SG CYS E 132 " pdb="FE3 SF4 E1274 " - pdb=" SG CYS E 171 " pdb=" SF4 E1275 " pdb="FE2 SF4 E1275 " - pdb=" SG CYS E 252 " pdb="FE1 SF4 E1275 " - pdb=" SG CYS E 249 " pdb="FE3 SF4 E1275 " - pdb=" SG CYS E 230 " pdb="FE4 SF4 E1275 " - pdb=" SG CYS E 255 " pdb=" SF4 E1276 " pdb="FE3 SF4 E1276 " - pdb=" SG CYS E 259 " pdb="FE4 SF4 E1276 " - pdb=" SG CYS E 226 " pdb="FE1 SF4 E1276 " - pdb=" SG CYS E 220 " pdb="FE2 SF4 E1276 " - pdb=" SG CYS E 223 " pdb=" SF4 F1282 " pdb="FE1 SF4 F1282 " - pdb=" SG CYS F 104 " pdb="FE4 SF4 F1282 " - pdb=" SG CYS F 134 " pdb="FE3 SF4 F1282 " - pdb=" SG CYS F 192 " pdb="FE2 SF4 F1282 " - pdb=" SG CYS F 195 " pdb=" SF4 H1274 " pdb="FE1 SF4 H1274 " - pdb=" SG CYS H 57 " pdb="FE2 SF4 H1274 " - pdb=" SG CYS H 132 " pdb="FE3 SF4 H1274 " - pdb=" SG CYS H 171 " pdb=" SF4 H1275 " pdb="FE2 SF4 H1275 " - pdb=" SG CYS H 252 " pdb="FE1 SF4 H1275 " - pdb=" SG CYS H 249 " pdb="FE3 SF4 H1275 " - pdb=" SG CYS H 230 " pdb="FE4 SF4 H1275 " - pdb=" SG CYS H 255 " pdb=" SF4 H1276 " pdb="FE3 SF4 H1276 " - pdb=" SG CYS H 259 " pdb="FE4 SF4 H1276 " - pdb=" SG CYS H 226 " pdb="FE1 SF4 H1276 " - pdb=" SG CYS H 220 " pdb="FE2 SF4 H1276 " - pdb=" SG CYS H 223 " pdb=" SF4 I1282 " pdb="FE1 SF4 I1282 " - pdb=" SG CYS I 104 " pdb="FE4 SF4 I1282 " - pdb=" SG CYS I 134 " pdb="FE3 SF4 I1282 " - pdb=" SG CYS I 192 " pdb="FE2 SF4 I1282 " - pdb=" SG CYS I 195 " pdb=" SF4 K1274 " pdb="FE1 SF4 K1274 " - pdb=" SG CYS K 57 " pdb="FE2 SF4 K1274 " - pdb=" SG CYS K 132 " pdb="FE3 SF4 K1274 " - pdb=" SG CYS K 171 " pdb=" SF4 K1275 " pdb="FE2 SF4 K1275 " - pdb=" SG CYS K 252 " pdb="FE1 SF4 K1275 " - pdb=" SG CYS K 249 " pdb="FE3 SF4 K1275 " - pdb=" SG CYS K 230 " pdb="FE4 SF4 K1275 " - pdb=" SG CYS K 255 " pdb=" SF4 K1276 " pdb="FE3 SF4 K1276 " - pdb=" SG CYS K 259 " pdb="FE4 SF4 K1276 " - pdb=" SG CYS K 226 " pdb="FE1 SF4 K1276 " - pdb=" SG CYS K 220 " pdb="FE2 SF4 K1276 " - pdb=" SG CYS K 223 " pdb=" SF4 L1282 " pdb="FE1 SF4 L1282 " - pdb=" SG CYS L 104 " pdb="FE4 SF4 L1282 " - pdb=" SG CYS L 134 " pdb="FE3 SF4 L1282 " - pdb=" SG CYS L 192 " pdb="FE2 SF4 L1282 " - pdb=" SG CYS L 195 " pdb=" SF4 N1274 " pdb="FE1 SF4 N1274 " - pdb=" SG CYS N 57 " pdb="FE2 SF4 N1274 " - pdb=" SG CYS N 132 " pdb="FE3 SF4 N1274 " - pdb=" SG CYS N 171 " pdb=" SF4 N1275 " pdb="FE2 SF4 N1275 " - pdb=" SG CYS N 252 " pdb="FE1 SF4 N1275 " - pdb=" SG CYS N 249 " pdb="FE3 SF4 N1275 " - pdb=" SG CYS N 230 " pdb="FE4 SF4 N1275 " - pdb=" SG CYS N 255 " pdb=" SF4 N1276 " pdb="FE3 SF4 N1276 " - pdb=" SG CYS N 259 " pdb="FE4 SF4 N1276 " - pdb=" SG CYS N 226 " pdb="FE1 SF4 N1276 " - pdb=" SG CYS N 220 " pdb="FE2 SF4 N1276 " - pdb=" SG CYS N 223 " pdb=" SF4 O1282 " pdb="FE1 SF4 O1282 " - pdb=" SG CYS O 104 " pdb="FE4 SF4 O1282 " - pdb=" SG CYS O 134 " pdb="FE3 SF4 O1282 " - pdb=" SG CYS O 192 " pdb="FE2 SF4 O1282 " - pdb=" SG CYS O 195 " pdb=" SF4 Q1274 " pdb="FE1 SF4 Q1274 " - pdb=" SG CYS Q 57 " pdb="FE2 SF4 Q1274 " - pdb=" SG CYS Q 132 " pdb="FE3 SF4 Q1274 " - pdb=" SG CYS Q 171 " pdb=" SF4 Q1275 " pdb="FE2 SF4 Q1275 " - pdb=" SG CYS Q 252 " pdb="FE1 SF4 Q1275 " - pdb=" SG CYS Q 249 " pdb="FE3 SF4 Q1275 " - pdb=" SG CYS Q 230 " pdb="FE4 SF4 Q1275 " - pdb=" SG CYS Q 255 " pdb=" SF4 Q1276 " pdb="FE3 SF4 Q1276 " - pdb=" SG CYS Q 259 " pdb="FE4 SF4 Q1276 " - pdb=" SG CYS Q 226 " pdb="FE1 SF4 Q1276 " - pdb=" SG CYS Q 220 " pdb="FE2 SF4 Q1276 " - pdb=" SG CYS Q 223 " pdb=" SF4 R1282 " pdb="FE1 SF4 R1282 " - pdb=" SG CYS R 104 " pdb="FE4 SF4 R1282 " - pdb=" SG CYS R 134 " pdb="FE3 SF4 R1282 " - pdb=" SG CYS R 192 " pdb="FE2 SF4 R1282 " - pdb=" SG CYS R 195 " pdb=" SF4 T1274 " pdb="FE1 SF4 T1274 " - pdb=" SG CYS T 57 " pdb="FE2 SF4 T1274 " - pdb=" SG CYS T 132 " pdb="FE3 SF4 T1274 " - pdb=" SG CYS T 171 " pdb=" SF4 T1275 " pdb="FE2 SF4 T1275 " - pdb=" SG CYS T 252 " pdb="FE1 SF4 T1275 " - pdb=" SG CYS T 249 " pdb="FE3 SF4 T1275 " - pdb=" SG CYS T 230 " pdb="FE4 SF4 T1275 " - pdb=" SG CYS T 255 " pdb=" SF4 T1276 " pdb="FE3 SF4 T1276 " - pdb=" SG CYS T 259 " pdb="FE4 SF4 T1276 " - pdb=" SG CYS T 226 " pdb="FE1 SF4 T1276 " - pdb=" SG CYS T 220 " pdb="FE2 SF4 T1276 " - pdb=" SG CYS T 223 " pdb=" SF4 U1282 " pdb="FE1 SF4 U1282 " - pdb=" SG CYS U 104 " pdb="FE4 SF4 U1282 " - pdb=" SG CYS U 134 " pdb="FE3 SF4 U1282 " - pdb=" SG CYS U 192 " pdb="FE2 SF4 U1282 " - pdb=" SG CYS U 195 " pdb=" SF4 W1274 " pdb="FE1 SF4 W1274 " - pdb=" SG CYS W 57 " pdb="FE2 SF4 W1274 " - pdb=" SG CYS W 132 " pdb="FE3 SF4 W1274 " - pdb=" SG CYS W 171 " pdb=" SF4 W1275 " pdb="FE2 SF4 W1275 " - pdb=" SG CYS W 252 " pdb="FE1 SF4 W1275 " - pdb=" SG CYS W 249 " pdb="FE3 SF4 W1275 " - pdb=" SG CYS W 230 " pdb="FE4 SF4 W1275 " - pdb=" SG CYS W 255 " pdb=" SF4 W1276 " pdb="FE3 SF4 W1276 " - pdb=" SG CYS W 259 " pdb="FE4 SF4 W1276 " - pdb=" SG CYS W 226 " pdb="FE1 SF4 W1276 " - pdb=" SG CYS W 220 " pdb="FE2 SF4 W1276 " - pdb=" SG CYS W 223 " pdb=" SF4 X1282 " pdb="FE1 SF4 X1282 " - pdb=" SG CYS X 104 " pdb="FE4 SF4 X1282 " - pdb=" SG CYS X 134 " pdb="FE3 SF4 X1282 " - pdb=" SG CYS X 192 " pdb="FE2 SF4 X1282 " - pdb=" SG CYS X 195 " pdb=" SF4 Z1274 " pdb="FE1 SF4 Z1274 " - pdb=" SG CYS Z 57 " pdb="FE2 SF4 Z1274 " - pdb=" SG CYS Z 132 " pdb="FE3 SF4 Z1274 " - pdb=" SG CYS Z 171 " pdb=" SF4 Z1275 " pdb="FE2 SF4 Z1275 " - pdb=" SG CYS Z 252 " pdb="FE1 SF4 Z1275 " - pdb=" SG CYS Z 249 " pdb="FE3 SF4 Z1275 " - pdb=" SG CYS Z 230 " pdb="FE4 SF4 Z1275 " - pdb=" SG CYS Z 255 " pdb=" SF4 Z1276 " pdb="FE3 SF4 Z1276 " - pdb=" SG CYS Z 259 " pdb="FE4 SF4 Z1276 " - pdb=" SG CYS Z 226 " pdb="FE1 SF4 Z1276 " - pdb=" SG CYS Z 220 " pdb="FE2 SF4 Z1276 " - pdb=" SG CYS Z 223 " Number of angles added : 540 Zn2+ tetrahedral coordination pdb=" ZN 21277 " pdb="ZN ZN 21277 " - pdb=" SG CYS 2 208 " pdb="ZN ZN 21277 " - pdb=" SG CYS 5 208 " pdb="ZN ZN 21277 " - pdb=" SG CYS 2 206 " pdb="ZN ZN 21277 " - pdb=" SG CYS 5 206 " pdb=" ZN 51277 " pdb="ZN ZN 51277 " - pdb=" SG CYS 5 208 " pdb="ZN ZN 51277 " - pdb=" SG CYS 2 208 " pdb="ZN ZN 51277 " - pdb=" SG CYS 5 206 " pdb="ZN ZN 51277 " - pdb=" SG CYS 2 206 " pdb=" ZN 81277 " pdb="ZN ZN 81277 " - pdb=" SG CYS 8 208 " pdb="ZN ZN 81277 " - pdb=" SG CYS Z 208 " pdb="ZN ZN 81277 " - pdb=" SG CYS 8 206 " pdb="ZN ZN 81277 " - pdb=" SG CYS Z 206 " pdb=" ZN B1277 " pdb="ZN ZN B1277 " - pdb=" SG CYS B 208 " pdb="ZN ZN B1277 " - pdb=" SG CYS K 208 " pdb="ZN ZN B1277 " - pdb=" SG CYS B 206 " pdb="ZN ZN B1277 " - pdb=" SG CYS K 206 " pdb=" ZN E1277 " pdb="ZN ZN E1277 " - pdb=" SG CYS E 208 " pdb="ZN ZN E1277 " - pdb=" SG CYS H 208 " pdb="ZN ZN E1277 " - pdb=" SG CYS E 206 " pdb="ZN ZN E1277 " - pdb=" SG CYS H 206 " pdb=" ZN H1277 " pdb="ZN ZN H1277 " - pdb=" SG CYS H 208 " pdb="ZN ZN H1277 " - pdb=" SG CYS E 208 " pdb="ZN ZN H1277 " - pdb=" SG CYS H 206 " pdb="ZN ZN H1277 " - pdb=" SG CYS E 206 " pdb=" ZN K1277 " pdb="ZN ZN K1277 " - pdb=" SG CYS K 208 " pdb="ZN ZN K1277 " - pdb=" SG CYS B 208 " pdb="ZN ZN K1277 " - pdb=" SG CYS K 206 " pdb="ZN ZN K1277 " - pdb=" SG CYS B 206 " pdb=" ZN N1277 " pdb="ZN ZN N1277 " - pdb=" SG CYS N 208 " pdb="ZN ZN N1277 " - pdb=" SG CYS W 208 " pdb="ZN ZN N1277 " - pdb=" SG CYS N 206 " pdb="ZN ZN N1277 " - pdb=" SG CYS W 206 " pdb=" ZN Q1277 " pdb="ZN ZN Q1277 " - pdb=" SG CYS Q 208 " pdb="ZN ZN Q1277 " - pdb=" SG CYS T 208 " pdb="ZN ZN Q1277 " - pdb=" SG CYS Q 206 " pdb="ZN ZN Q1277 " - pdb=" SG CYS T 206 " pdb=" ZN T1277 " pdb="ZN ZN T1277 " - pdb=" SG CYS T 208 " pdb="ZN ZN T1277 " - pdb=" SG CYS Q 208 " pdb="ZN ZN T1277 " - pdb=" SG CYS T 206 " pdb="ZN ZN T1277 " - pdb=" SG CYS Q 206 " pdb=" ZN W1277 " pdb="ZN ZN W1277 " - pdb=" SG CYS W 208 " pdb="ZN ZN W1277 " - pdb=" SG CYS N 208 " pdb="ZN ZN W1277 " - pdb=" SG CYS W 206 " pdb="ZN ZN W1277 " - pdb=" SG CYS N 206 " pdb=" ZN Z1277 " pdb="ZN ZN Z1277 " - pdb=" SG CYS Z 208 " pdb="ZN ZN Z1277 " - pdb=" SG CYS 8 208 " pdb="ZN ZN Z1277 " - pdb=" SG CYS Z 206 " pdb="ZN ZN Z1277 " - pdb=" SG CYS 8 206 " Number of angles added : 72 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 444 helices and 84 sheets defined 43.1% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.59 Creating SS restraints... Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 52 through 62 Proline residue: A 56 - end of helix removed outlier: 3.976A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 88 through 117 Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 120 through 145 removed outlier: 3.982A pdb=" N ALA A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 196 removed outlier: 3.689A pdb=" N ARG A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.511A pdb=" N GLU A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 261 through 267 Processing helix chain 'A' and resid 276 through 299 removed outlier: 3.677A pdb=" N ALA A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 361 removed outlier: 3.524A pdb=" N ASN A 354 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Proline residue: A 356 - end of helix removed outlier: 3.796A pdb=" N GLY A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 377 Proline residue: A 371 - end of helix removed outlier: 3.562A pdb=" N ARG A 375 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'B' and resid 59 through 66 Processing helix chain 'B' and resid 68 through 76 removed outlier: 4.965A pdb=" N GLU B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 122 removed outlier: 4.076A pdb=" N GLU B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 158 through 161 No H-bonds generated for 'chain 'B' and resid 158 through 161' Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 192 through 201 Proline residue: B 195 - end of helix Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 225 through 228 No H-bonds generated for 'chain 'B' and resid 225 through 228' Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'B' and resid 267 through 272 removed outlier: 3.524A pdb=" N LYS B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 81 through 90 removed outlier: 3.804A pdb=" N LYS C 86 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 89 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 90 " --> pdb=" O LYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.910A pdb=" N LYS C 111 " --> pdb=" O MET C 107 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET C 112 " --> pdb=" O GLY C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 125 No H-bonds generated for 'chain 'C' and resid 122 through 125' Processing helix chain 'C' and resid 140 through 148 removed outlier: 3.769A pdb=" N PHE C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.507A pdb=" N ILE C 194 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 236 Processing helix chain 'C' and resid 251 through 274 removed outlier: 3.615A pdb=" N LYS C 267 " --> pdb=" O GLU C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 47 Processing helix chain 'D' and resid 52 through 62 Proline residue: D 56 - end of helix removed outlier: 3.975A pdb=" N ARG D 61 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE D 62 " --> pdb=" O MET D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 88 through 117 Proline residue: D 115 - end of helix Processing helix chain 'D' and resid 120 through 145 removed outlier: 3.982A pdb=" N ALA D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP D 125 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 196 removed outlier: 3.689A pdb=" N ARG D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Proline residue: D 180 - end of helix removed outlier: 3.512A pdb=" N GLU D 187 " --> pdb=" O ASN D 183 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP D 195 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 No H-bonds generated for 'chain 'D' and resid 232 through 235' Processing helix chain 'D' and resid 239 through 244 Processing helix chain 'D' and resid 261 through 267 Processing helix chain 'D' and resid 276 through 299 removed outlier: 3.677A pdb=" N ALA D 284 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D 293 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 361 removed outlier: 3.523A pdb=" N ASN D 354 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Proline residue: D 356 - end of helix removed outlier: 3.795A pdb=" N GLY D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Proline residue: D 360 - end of helix Processing helix chain 'D' and resid 367 through 377 Proline residue: D 371 - end of helix removed outlier: 3.562A pdb=" N ARG D 375 " --> pdb=" O HIS D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'E' and resid 59 through 66 Processing helix chain 'E' and resid 68 through 76 removed outlier: 4.966A pdb=" N GLU E 73 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 122 removed outlier: 4.076A pdb=" N GLU E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 134 Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 158 through 161 No H-bonds generated for 'chain 'E' and resid 158 through 161' Processing helix chain 'E' and resid 175 through 186 Processing helix chain 'E' and resid 192 through 201 Proline residue: E 195 - end of helix Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 225 through 228 No H-bonds generated for 'chain 'E' and resid 225 through 228' Processing helix chain 'E' and resid 246 through 248 No H-bonds generated for 'chain 'E' and resid 246 through 248' Processing helix chain 'E' and resid 254 through 258 Processing helix chain 'E' and resid 267 through 272 removed outlier: 3.525A pdb=" N LYS E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 22 Processing helix chain 'F' and resid 28 through 39 Processing helix chain 'F' and resid 65 through 71 Processing helix chain 'F' and resid 81 through 90 removed outlier: 3.804A pdb=" N LYS F 86 " --> pdb=" O MET F 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG F 90 " --> pdb=" O LYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 114 removed outlier: 3.911A pdb=" N LYS F 111 " --> pdb=" O MET F 107 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET F 112 " --> pdb=" O GLY F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 125 No H-bonds generated for 'chain 'F' and resid 122 through 125' Processing helix chain 'F' and resid 140 through 148 removed outlier: 3.768A pdb=" N PHE F 146 " --> pdb=" O SER F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 184 Processing helix chain 'F' and resid 190 through 194 removed outlier: 3.507A pdb=" N ILE F 194 " --> pdb=" O GLY F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 236 Processing helix chain 'F' and resid 251 through 274 removed outlier: 3.615A pdb=" N LYS F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 47 Processing helix chain 'G' and resid 52 through 62 Proline residue: G 56 - end of helix removed outlier: 3.976A pdb=" N ARG G 61 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE G 62 " --> pdb=" O MET G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 82 Processing helix chain 'G' and resid 88 through 117 Proline residue: G 115 - end of helix Processing helix chain 'G' and resid 120 through 145 removed outlier: 3.981A pdb=" N ALA G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP G 125 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL G 140 " --> pdb=" O ASN G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 196 removed outlier: 3.688A pdb=" N ARG G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) Proline residue: G 180 - end of helix removed outlier: 3.511A pdb=" N GLU G 187 " --> pdb=" O ASN G 183 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU G 194 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP G 195 " --> pdb=" O GLY G 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS G 196 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 235 No H-bonds generated for 'chain 'G' and resid 232 through 235' Processing helix chain 'G' and resid 239 through 244 Processing helix chain 'G' and resid 261 through 267 Processing helix chain 'G' and resid 276 through 299 removed outlier: 3.677A pdb=" N ALA G 284 " --> pdb=" O HIS G 280 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 293 " --> pdb=" O THR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 361 removed outlier: 3.524A pdb=" N ASN G 354 " --> pdb=" O PRO G 350 " (cutoff:3.500A) Proline residue: G 356 - end of helix removed outlier: 3.796A pdb=" N GLY G 359 " --> pdb=" O ILE G 355 " (cutoff:3.500A) Proline residue: G 360 - end of helix Processing helix chain 'G' and resid 367 through 377 Proline residue: G 371 - end of helix removed outlier: 3.562A pdb=" N ARG G 375 " --> pdb=" O HIS G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 385 Processing helix chain 'H' and resid 59 through 66 Processing helix chain 'H' and resid 68 through 76 removed outlier: 4.965A pdb=" N GLU H 73 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 122 removed outlier: 4.076A pdb=" N GLU H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 134 Processing helix chain 'H' and resid 137 through 141 Processing helix chain 'H' and resid 158 through 161 No H-bonds generated for 'chain 'H' and resid 158 through 161' Processing helix chain 'H' and resid 175 through 186 Processing helix chain 'H' and resid 192 through 201 Proline residue: H 195 - end of helix Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'H' and resid 225 through 228 No H-bonds generated for 'chain 'H' and resid 225 through 228' Processing helix chain 'H' and resid 246 through 248 No H-bonds generated for 'chain 'H' and resid 246 through 248' Processing helix chain 'H' and resid 254 through 258 Processing helix chain 'H' and resid 267 through 272 removed outlier: 3.524A pdb=" N LYS H 271 " --> pdb=" O GLU H 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 22 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 65 through 71 Processing helix chain 'I' and resid 81 through 90 removed outlier: 3.805A pdb=" N LYS I 86 " --> pdb=" O MET I 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL I 89 " --> pdb=" O LYS I 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG I 90 " --> pdb=" O LYS I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 114 removed outlier: 3.910A pdb=" N LYS I 111 " --> pdb=" O MET I 107 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET I 112 " --> pdb=" O GLY I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 125 No H-bonds generated for 'chain 'I' and resid 122 through 125' Processing helix chain 'I' and resid 140 through 148 removed outlier: 3.769A pdb=" N PHE I 146 " --> pdb=" O SER I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 184 Processing helix chain 'I' and resid 190 through 194 removed outlier: 3.506A pdb=" N ILE I 194 " --> pdb=" O GLY I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 236 Processing helix chain 'I' and resid 251 through 274 removed outlier: 3.615A pdb=" N LYS I 267 " --> pdb=" O GLU I 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 47 Processing helix chain 'J' and resid 52 through 62 Proline residue: J 56 - end of helix removed outlier: 3.976A pdb=" N ARG J 61 " --> pdb=" O VAL J 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE J 62 " --> pdb=" O MET J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 82 Processing helix chain 'J' and resid 88 through 117 Proline residue: J 115 - end of helix Processing helix chain 'J' and resid 120 through 145 removed outlier: 3.981A pdb=" N ALA J 124 " --> pdb=" O GLU J 120 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP J 125 " --> pdb=" O ASN J 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR J 139 " --> pdb=" O LYS J 135 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL J 140 " --> pdb=" O ASN J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 196 removed outlier: 3.688A pdb=" N ARG J 174 " --> pdb=" O ARG J 170 " (cutoff:3.500A) Proline residue: J 180 - end of helix removed outlier: 3.512A pdb=" N GLU J 187 " --> pdb=" O ASN J 183 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU J 194 " --> pdb=" O ILE J 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP J 195 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS J 196 " --> pdb=" O LEU J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 235 No H-bonds generated for 'chain 'J' and resid 232 through 235' Processing helix chain 'J' and resid 239 through 244 Processing helix chain 'J' and resid 261 through 267 Processing helix chain 'J' and resid 276 through 299 removed outlier: 3.677A pdb=" N ALA J 284 " --> pdb=" O HIS J 280 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER J 292 " --> pdb=" O LYS J 288 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG J 293 " --> pdb=" O THR J 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 361 removed outlier: 3.524A pdb=" N ASN J 354 " --> pdb=" O PRO J 350 " (cutoff:3.500A) Proline residue: J 356 - end of helix removed outlier: 3.797A pdb=" N GLY J 359 " --> pdb=" O ILE J 355 " (cutoff:3.500A) Proline residue: J 360 - end of helix Processing helix chain 'J' and resid 367 through 377 Proline residue: J 371 - end of helix removed outlier: 3.562A pdb=" N ARG J 375 " --> pdb=" O HIS J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 381 through 385 Processing helix chain 'K' and resid 59 through 66 Processing helix chain 'K' and resid 68 through 76 removed outlier: 4.965A pdb=" N GLU K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 122 removed outlier: 4.076A pdb=" N GLU K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 134 Processing helix chain 'K' and resid 137 through 141 Processing helix chain 'K' and resid 158 through 161 No H-bonds generated for 'chain 'K' and resid 158 through 161' Processing helix chain 'K' and resid 175 through 186 Processing helix chain 'K' and resid 192 through 201 Proline residue: K 195 - end of helix Processing helix chain 'K' and resid 208 through 213 Processing helix chain 'K' and resid 225 through 228 No H-bonds generated for 'chain 'K' and resid 225 through 228' Processing helix chain 'K' and resid 246 through 248 No H-bonds generated for 'chain 'K' and resid 246 through 248' Processing helix chain 'K' and resid 254 through 258 Processing helix chain 'K' and resid 267 through 272 removed outlier: 3.525A pdb=" N LYS K 271 " --> pdb=" O GLU K 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 Processing helix chain 'L' and resid 28 through 39 Processing helix chain 'L' and resid 65 through 71 Processing helix chain 'L' and resid 81 through 90 removed outlier: 3.805A pdb=" N LYS L 86 " --> pdb=" O MET L 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL L 89 " --> pdb=" O LYS L 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG L 90 " --> pdb=" O LYS L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 114 removed outlier: 3.911A pdb=" N LYS L 111 " --> pdb=" O MET L 107 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET L 112 " --> pdb=" O GLY L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 125 No H-bonds generated for 'chain 'L' and resid 122 through 125' Processing helix chain 'L' and resid 140 through 148 removed outlier: 3.768A pdb=" N PHE L 146 " --> pdb=" O SER L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 184 Processing helix chain 'L' and resid 190 through 194 removed outlier: 3.506A pdb=" N ILE L 194 " --> pdb=" O GLY L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 236 Processing helix chain 'L' and resid 251 through 274 removed outlier: 3.615A pdb=" N LYS L 267 " --> pdb=" O GLU L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 47 Processing helix chain 'M' and resid 52 through 62 Proline residue: M 56 - end of helix removed outlier: 3.976A pdb=" N ARG M 61 " --> pdb=" O VAL M 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE M 62 " --> pdb=" O MET M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 82 Processing helix chain 'M' and resid 88 through 117 Proline residue: M 115 - end of helix Processing helix chain 'M' and resid 120 through 145 removed outlier: 3.982A pdb=" N ALA M 124 " --> pdb=" O GLU M 120 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP M 125 " --> pdb=" O ASN M 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL M 140 " --> pdb=" O ASN M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 196 removed outlier: 3.688A pdb=" N ARG M 174 " --> pdb=" O ARG M 170 " (cutoff:3.500A) Proline residue: M 180 - end of helix removed outlier: 3.512A pdb=" N GLU M 187 " --> pdb=" O ASN M 183 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU M 194 " --> pdb=" O ILE M 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP M 195 " --> pdb=" O GLY M 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS M 196 " --> pdb=" O LEU M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 235 No H-bonds generated for 'chain 'M' and resid 232 through 235' Processing helix chain 'M' and resid 239 through 244 Processing helix chain 'M' and resid 261 through 267 Processing helix chain 'M' and resid 276 through 299 removed outlier: 3.678A pdb=" N ALA M 284 " --> pdb=" O HIS M 280 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER M 292 " --> pdb=" O LYS M 288 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG M 293 " --> pdb=" O THR M 289 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 361 removed outlier: 3.524A pdb=" N ASN M 354 " --> pdb=" O PRO M 350 " (cutoff:3.500A) Proline residue: M 356 - end of helix removed outlier: 3.797A pdb=" N GLY M 359 " --> pdb=" O ILE M 355 " (cutoff:3.500A) Proline residue: M 360 - end of helix Processing helix chain 'M' and resid 367 through 377 Proline residue: M 371 - end of helix removed outlier: 3.562A pdb=" N ARG M 375 " --> pdb=" O HIS M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 381 through 385 Processing helix chain 'N' and resid 59 through 66 Processing helix chain 'N' and resid 68 through 76 removed outlier: 4.964A pdb=" N GLU N 73 " --> pdb=" O ASP N 69 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 122 removed outlier: 4.077A pdb=" N GLU N 121 " --> pdb=" O LYS N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 134 Processing helix chain 'N' and resid 137 through 141 Processing helix chain 'N' and resid 158 through 161 No H-bonds generated for 'chain 'N' and resid 158 through 161' Processing helix chain 'N' and resid 175 through 186 Processing helix chain 'N' and resid 192 through 201 Proline residue: N 195 - end of helix Processing helix chain 'N' and resid 208 through 213 Processing helix chain 'N' and resid 225 through 228 No H-bonds generated for 'chain 'N' and resid 225 through 228' Processing helix chain 'N' and resid 246 through 248 No H-bonds generated for 'chain 'N' and resid 246 through 248' Processing helix chain 'N' and resid 254 through 258 Processing helix chain 'N' and resid 267 through 272 removed outlier: 3.523A pdb=" N LYS N 271 " --> pdb=" O GLU N 267 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 22 Processing helix chain 'O' and resid 28 through 39 Processing helix chain 'O' and resid 65 through 71 Processing helix chain 'O' and resid 81 through 90 removed outlier: 3.804A pdb=" N LYS O 86 " --> pdb=" O MET O 83 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL O 89 " --> pdb=" O LYS O 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG O 90 " --> pdb=" O LYS O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 114 removed outlier: 3.911A pdb=" N LYS O 111 " --> pdb=" O MET O 107 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET O 112 " --> pdb=" O GLY O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 125 No H-bonds generated for 'chain 'O' and resid 122 through 125' Processing helix chain 'O' and resid 140 through 148 removed outlier: 3.768A pdb=" N PHE O 146 " --> pdb=" O SER O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 184 Processing helix chain 'O' and resid 190 through 194 removed outlier: 3.507A pdb=" N ILE O 194 " --> pdb=" O GLY O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 224 through 236 Processing helix chain 'O' and resid 251 through 274 removed outlier: 3.615A pdb=" N LYS O 267 " --> pdb=" O GLU O 263 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 47 Processing helix chain 'P' and resid 52 through 62 Proline residue: P 56 - end of helix removed outlier: 3.975A pdb=" N ARG P 61 " --> pdb=" O VAL P 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE P 62 " --> pdb=" O MET P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 82 Processing helix chain 'P' and resid 88 through 117 Proline residue: P 115 - end of helix Processing helix chain 'P' and resid 120 through 145 removed outlier: 3.982A pdb=" N ALA P 124 " --> pdb=" O GLU P 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP P 125 " --> pdb=" O ASN P 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR P 139 " --> pdb=" O LYS P 135 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL P 140 " --> pdb=" O ASN P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 196 removed outlier: 3.689A pdb=" N ARG P 174 " --> pdb=" O ARG P 170 " (cutoff:3.500A) Proline residue: P 180 - end of helix removed outlier: 3.511A pdb=" N GLU P 187 " --> pdb=" O ASN P 183 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU P 194 " --> pdb=" O ILE P 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP P 195 " --> pdb=" O GLY P 191 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS P 196 " --> pdb=" O LEU P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 232 through 235 No H-bonds generated for 'chain 'P' and resid 232 through 235' Processing helix chain 'P' and resid 239 through 244 Processing helix chain 'P' and resid 261 through 267 Processing helix chain 'P' and resid 276 through 299 removed outlier: 3.678A pdb=" N ALA P 284 " --> pdb=" O HIS P 280 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER P 292 " --> pdb=" O LYS P 288 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG P 293 " --> pdb=" O THR P 289 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 361 removed outlier: 3.524A pdb=" N ASN P 354 " --> pdb=" O PRO P 350 " (cutoff:3.500A) Proline residue: P 356 - end of helix removed outlier: 3.796A pdb=" N GLY P 359 " --> pdb=" O ILE P 355 " (cutoff:3.500A) Proline residue: P 360 - end of helix Processing helix chain 'P' and resid 367 through 377 Proline residue: P 371 - end of helix removed outlier: 3.562A pdb=" N ARG P 375 " --> pdb=" O HIS P 372 " (cutoff:3.500A) Processing helix chain 'P' and resid 381 through 385 Processing helix chain 'Q' and resid 59 through 66 Processing helix chain 'Q' and resid 68 through 76 removed outlier: 4.965A pdb=" N GLU Q 73 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR Q 76 " --> pdb=" O ALA Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 122 removed outlier: 4.076A pdb=" N GLU Q 121 " --> pdb=" O LYS Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 134 Processing helix chain 'Q' and resid 137 through 141 Processing helix chain 'Q' and resid 158 through 161 No H-bonds generated for 'chain 'Q' and resid 158 through 161' Processing helix chain 'Q' and resid 175 through 186 Processing helix chain 'Q' and resid 192 through 201 Proline residue: Q 195 - end of helix Processing helix chain 'Q' and resid 208 through 213 Processing helix chain 'Q' and resid 225 through 228 No H-bonds generated for 'chain 'Q' and resid 225 through 228' Processing helix chain 'Q' and resid 246 through 248 No H-bonds generated for 'chain 'Q' and resid 246 through 248' Processing helix chain 'Q' and resid 254 through 258 Processing helix chain 'Q' and resid 267 through 272 removed outlier: 3.525A pdb=" N LYS Q 271 " --> pdb=" O GLU Q 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 22 Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 65 through 71 Processing helix chain 'R' and resid 81 through 90 removed outlier: 3.804A pdb=" N LYS R 86 " --> pdb=" O MET R 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL R 89 " --> pdb=" O LYS R 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG R 90 " --> pdb=" O LYS R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 114 removed outlier: 3.910A pdb=" N LYS R 111 " --> pdb=" O MET R 107 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET R 112 " --> pdb=" O GLY R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 125 No H-bonds generated for 'chain 'R' and resid 122 through 125' Processing helix chain 'R' and resid 140 through 148 removed outlier: 3.768A pdb=" N PHE R 146 " --> pdb=" O SER R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 184 Processing helix chain 'R' and resid 190 through 194 removed outlier: 3.507A pdb=" N ILE R 194 " --> pdb=" O GLY R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 236 Processing helix chain 'R' and resid 251 through 274 removed outlier: 3.615A pdb=" N LYS R 267 " --> pdb=" O GLU R 263 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 47 Processing helix chain 'S' and resid 52 through 62 Proline residue: S 56 - end of helix removed outlier: 3.975A pdb=" N ARG S 61 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE S 62 " --> pdb=" O MET S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 82 Processing helix chain 'S' and resid 88 through 117 Proline residue: S 115 - end of helix Processing helix chain 'S' and resid 120 through 145 removed outlier: 3.983A pdb=" N ALA S 124 " --> pdb=" O GLU S 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP S 125 " --> pdb=" O ASN S 121 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR S 139 " --> pdb=" O LYS S 135 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL S 140 " --> pdb=" O ASN S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 196 removed outlier: 3.689A pdb=" N ARG S 174 " --> pdb=" O ARG S 170 " (cutoff:3.500A) Proline residue: S 180 - end of helix removed outlier: 3.510A pdb=" N GLU S 187 " --> pdb=" O ASN S 183 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU S 194 " --> pdb=" O ILE S 190 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP S 195 " --> pdb=" O GLY S 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS S 196 " --> pdb=" O LEU S 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 235 No H-bonds generated for 'chain 'S' and resid 232 through 235' Processing helix chain 'S' and resid 239 through 244 Processing helix chain 'S' and resid 261 through 267 Processing helix chain 'S' and resid 276 through 299 removed outlier: 3.677A pdb=" N ALA S 284 " --> pdb=" O HIS S 280 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER S 292 " --> pdb=" O LYS S 288 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG S 293 " --> pdb=" O THR S 289 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 361 removed outlier: 3.524A pdb=" N ASN S 354 " --> pdb=" O PRO S 350 " (cutoff:3.500A) Proline residue: S 356 - end of helix removed outlier: 3.797A pdb=" N GLY S 359 " --> pdb=" O ILE S 355 " (cutoff:3.500A) Proline residue: S 360 - end of helix Processing helix chain 'S' and resid 367 through 377 Proline residue: S 371 - end of helix removed outlier: 3.563A pdb=" N ARG S 375 " --> pdb=" O HIS S 372 " (cutoff:3.500A) Processing helix chain 'S' and resid 381 through 385 Processing helix chain 'T' and resid 59 through 66 Processing helix chain 'T' and resid 68 through 76 removed outlier: 4.965A pdb=" N GLU T 73 " --> pdb=" O ASP T 69 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR T 76 " --> pdb=" O ALA T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 110 through 122 removed outlier: 4.076A pdb=" N GLU T 121 " --> pdb=" O LYS T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 130 through 134 Processing helix chain 'T' and resid 137 through 141 Processing helix chain 'T' and resid 158 through 161 No H-bonds generated for 'chain 'T' and resid 158 through 161' Processing helix chain 'T' and resid 175 through 186 Processing helix chain 'T' and resid 192 through 201 Proline residue: T 195 - end of helix Processing helix chain 'T' and resid 208 through 213 Processing helix chain 'T' and resid 225 through 228 No H-bonds generated for 'chain 'T' and resid 225 through 228' Processing helix chain 'T' and resid 246 through 248 No H-bonds generated for 'chain 'T' and resid 246 through 248' Processing helix chain 'T' and resid 254 through 258 Processing helix chain 'T' and resid 267 through 272 removed outlier: 3.525A pdb=" N LYS T 271 " --> pdb=" O GLU T 267 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 22 Processing helix chain 'U' and resid 28 through 39 Processing helix chain 'U' and resid 65 through 71 Processing helix chain 'U' and resid 81 through 90 removed outlier: 3.805A pdb=" N LYS U 86 " --> pdb=" O MET U 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL U 89 " --> pdb=" O LYS U 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG U 90 " --> pdb=" O LYS U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 103 through 114 removed outlier: 3.910A pdb=" N LYS U 111 " --> pdb=" O MET U 107 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET U 112 " --> pdb=" O GLY U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 122 through 125 No H-bonds generated for 'chain 'U' and resid 122 through 125' Processing helix chain 'U' and resid 140 through 148 removed outlier: 3.769A pdb=" N PHE U 146 " --> pdb=" O SER U 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 181 through 184 Processing helix chain 'U' and resid 190 through 194 removed outlier: 3.506A pdb=" N ILE U 194 " --> pdb=" O GLY U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 224 through 236 Processing helix chain 'U' and resid 251 through 274 removed outlier: 3.615A pdb=" N LYS U 267 " --> pdb=" O GLU U 263 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 47 Processing helix chain 'V' and resid 52 through 62 Proline residue: V 56 - end of helix removed outlier: 3.975A pdb=" N ARG V 61 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE V 62 " --> pdb=" O MET V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 82 Processing helix chain 'V' and resid 88 through 117 Proline residue: V 115 - end of helix Processing helix chain 'V' and resid 120 through 145 removed outlier: 3.982A pdb=" N ALA V 124 " --> pdb=" O GLU V 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP V 125 " --> pdb=" O ASN V 121 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR V 139 " --> pdb=" O LYS V 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL V 140 " --> pdb=" O ASN V 136 " (cutoff:3.500A) Processing helix chain 'V' and resid 165 through 196 removed outlier: 3.688A pdb=" N ARG V 174 " --> pdb=" O ARG V 170 " (cutoff:3.500A) Proline residue: V 180 - end of helix removed outlier: 3.511A pdb=" N GLU V 187 " --> pdb=" O ASN V 183 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU V 194 " --> pdb=" O ILE V 190 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP V 195 " --> pdb=" O GLY V 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS V 196 " --> pdb=" O LEU V 192 " (cutoff:3.500A) Processing helix chain 'V' and resid 232 through 235 No H-bonds generated for 'chain 'V' and resid 232 through 235' Processing helix chain 'V' and resid 239 through 244 Processing helix chain 'V' and resid 261 through 267 Processing helix chain 'V' and resid 276 through 299 removed outlier: 3.677A pdb=" N ALA V 284 " --> pdb=" O HIS V 280 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER V 292 " --> pdb=" O LYS V 288 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG V 293 " --> pdb=" O THR V 289 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 361 removed outlier: 3.524A pdb=" N ASN V 354 " --> pdb=" O PRO V 350 " (cutoff:3.500A) Proline residue: V 356 - end of helix removed outlier: 3.796A pdb=" N GLY V 359 " --> pdb=" O ILE V 355 " (cutoff:3.500A) Proline residue: V 360 - end of helix Processing helix chain 'V' and resid 367 through 377 Proline residue: V 371 - end of helix removed outlier: 3.561A pdb=" N ARG V 375 " --> pdb=" O HIS V 372 " (cutoff:3.500A) Processing helix chain 'V' and resid 381 through 385 Processing helix chain 'W' and resid 59 through 66 Processing helix chain 'W' and resid 68 through 76 removed outlier: 4.965A pdb=" N GLU W 73 " --> pdb=" O ASP W 69 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR W 76 " --> pdb=" O ALA W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 110 through 122 removed outlier: 4.076A pdb=" N GLU W 121 " --> pdb=" O LYS W 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 134 Processing helix chain 'W' and resid 137 through 141 Processing helix chain 'W' and resid 158 through 161 No H-bonds generated for 'chain 'W' and resid 158 through 161' Processing helix chain 'W' and resid 175 through 186 Processing helix chain 'W' and resid 192 through 201 Proline residue: W 195 - end of helix Processing helix chain 'W' and resid 208 through 213 Processing helix chain 'W' and resid 225 through 228 No H-bonds generated for 'chain 'W' and resid 225 through 228' Processing helix chain 'W' and resid 246 through 248 No H-bonds generated for 'chain 'W' and resid 246 through 248' Processing helix chain 'W' and resid 254 through 258 Processing helix chain 'W' and resid 267 through 272 removed outlier: 3.525A pdb=" N LYS W 271 " --> pdb=" O GLU W 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 22 Processing helix chain 'X' and resid 28 through 39 Processing helix chain 'X' and resid 65 through 71 Processing helix chain 'X' and resid 81 through 90 removed outlier: 3.805A pdb=" N LYS X 86 " --> pdb=" O MET X 83 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL X 89 " --> pdb=" O LYS X 86 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG X 90 " --> pdb=" O LYS X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 114 removed outlier: 3.911A pdb=" N LYS X 111 " --> pdb=" O MET X 107 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET X 112 " --> pdb=" O GLY X 108 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 125 No H-bonds generated for 'chain 'X' and resid 122 through 125' Processing helix chain 'X' and resid 140 through 148 removed outlier: 3.768A pdb=" N PHE X 146 " --> pdb=" O SER X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 181 through 184 Processing helix chain 'X' and resid 190 through 194 removed outlier: 3.507A pdb=" N ILE X 194 " --> pdb=" O GLY X 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 236 Processing helix chain 'X' and resid 251 through 274 removed outlier: 3.615A pdb=" N LYS X 267 " --> pdb=" O GLU X 263 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 47 Processing helix chain 'Y' and resid 52 through 62 Proline residue: Y 56 - end of helix removed outlier: 3.976A pdb=" N ARG Y 61 " --> pdb=" O VAL Y 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE Y 62 " --> pdb=" O MET Y 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 82 Processing helix chain 'Y' and resid 88 through 117 Proline residue: Y 115 - end of helix Processing helix chain 'Y' and resid 120 through 145 removed outlier: 3.982A pdb=" N ALA Y 124 " --> pdb=" O GLU Y 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP Y 125 " --> pdb=" O ASN Y 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR Y 139 " --> pdb=" O LYS Y 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL Y 140 " --> pdb=" O ASN Y 136 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 196 removed outlier: 3.689A pdb=" N ARG Y 174 " --> pdb=" O ARG Y 170 " (cutoff:3.500A) Proline residue: Y 180 - end of helix removed outlier: 3.512A pdb=" N GLU Y 187 " --> pdb=" O ASN Y 183 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU Y 194 " --> pdb=" O ILE Y 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP Y 195 " --> pdb=" O GLY Y 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS Y 196 " --> pdb=" O LEU Y 192 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 235 No H-bonds generated for 'chain 'Y' and resid 232 through 235' Processing helix chain 'Y' and resid 239 through 244 Processing helix chain 'Y' and resid 261 through 267 Processing helix chain 'Y' and resid 276 through 299 removed outlier: 3.678A pdb=" N ALA Y 284 " --> pdb=" O HIS Y 280 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER Y 292 " --> pdb=" O LYS Y 288 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG Y 293 " --> pdb=" O THR Y 289 " (cutoff:3.500A) Processing helix chain 'Y' and resid 350 through 361 removed outlier: 3.523A pdb=" N ASN Y 354 " --> pdb=" O PRO Y 350 " (cutoff:3.500A) Proline residue: Y 356 - end of helix removed outlier: 3.796A pdb=" N GLY Y 359 " --> pdb=" O ILE Y 355 " (cutoff:3.500A) Proline residue: Y 360 - end of helix Processing helix chain 'Y' and resid 367 through 377 Proline residue: Y 371 - end of helix removed outlier: 3.562A pdb=" N ARG Y 375 " --> pdb=" O HIS Y 372 " (cutoff:3.500A) Processing helix chain 'Y' and resid 381 through 385 Processing helix chain 'Z' and resid 59 through 66 Processing helix chain 'Z' and resid 68 through 76 removed outlier: 4.966A pdb=" N GLU Z 73 " --> pdb=" O ASP Z 69 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR Z 76 " --> pdb=" O ALA Z 72 " (cutoff:3.500A) Processing helix chain 'Z' and resid 110 through 122 removed outlier: 4.076A pdb=" N GLU Z 121 " --> pdb=" O LYS Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 134 Processing helix chain 'Z' and resid 137 through 141 Processing helix chain 'Z' and resid 158 through 161 No H-bonds generated for 'chain 'Z' and resid 158 through 161' Processing helix chain 'Z' and resid 175 through 186 Processing helix chain 'Z' and resid 192 through 201 Proline residue: Z 195 - end of helix Processing helix chain 'Z' and resid 208 through 213 Processing helix chain 'Z' and resid 225 through 228 No H-bonds generated for 'chain 'Z' and resid 225 through 228' Processing helix chain 'Z' and resid 246 through 248 No H-bonds generated for 'chain 'Z' and resid 246 through 248' Processing helix chain 'Z' and resid 254 through 258 Processing helix chain 'Z' and resid 267 through 272 removed outlier: 3.524A pdb=" N LYS Z 271 " --> pdb=" O GLU Z 267 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 22 Processing helix chain '0' and resid 28 through 39 Processing helix chain '0' and resid 65 through 71 Processing helix chain '0' and resid 81 through 90 removed outlier: 3.805A pdb=" N LYS 0 86 " --> pdb=" O MET 0 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL 0 89 " --> pdb=" O LYS 0 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG 0 90 " --> pdb=" O LYS 0 87 " (cutoff:3.500A) Processing helix chain '0' and resid 103 through 114 removed outlier: 3.910A pdb=" N LYS 0 111 " --> pdb=" O MET 0 107 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET 0 112 " --> pdb=" O GLY 0 108 " (cutoff:3.500A) Processing helix chain '0' and resid 122 through 125 No H-bonds generated for 'chain '0' and resid 122 through 125' Processing helix chain '0' and resid 140 through 148 removed outlier: 3.768A pdb=" N PHE 0 146 " --> pdb=" O SER 0 142 " (cutoff:3.500A) Processing helix chain '0' and resid 181 through 184 Processing helix chain '0' and resid 190 through 194 removed outlier: 3.507A pdb=" N ILE 0 194 " --> pdb=" O GLY 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 224 through 236 Processing helix chain '0' and resid 251 through 274 removed outlier: 3.616A pdb=" N LYS 0 267 " --> pdb=" O GLU 0 263 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 47 Processing helix chain '1' and resid 52 through 62 Proline residue: 1 56 - end of helix removed outlier: 3.975A pdb=" N ARG 1 61 " --> pdb=" O VAL 1 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE 1 62 " --> pdb=" O MET 1 58 " (cutoff:3.500A) Processing helix chain '1' and resid 67 through 82 Processing helix chain '1' and resid 88 through 117 Proline residue: 1 115 - end of helix Processing helix chain '1' and resid 120 through 145 removed outlier: 3.982A pdb=" N ALA 1 124 " --> pdb=" O GLU 1 120 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP 1 125 " --> pdb=" O ASN 1 121 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR 1 139 " --> pdb=" O LYS 1 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL 1 140 " --> pdb=" O ASN 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 165 through 196 removed outlier: 3.689A pdb=" N ARG 1 174 " --> pdb=" O ARG 1 170 " (cutoff:3.500A) Proline residue: 1 180 - end of helix removed outlier: 3.512A pdb=" N GLU 1 187 " --> pdb=" O ASN 1 183 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU 1 194 " --> pdb=" O ILE 1 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP 1 195 " --> pdb=" O GLY 1 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS 1 196 " --> pdb=" O LEU 1 192 " (cutoff:3.500A) Processing helix chain '1' and resid 232 through 235 No H-bonds generated for 'chain '1' and resid 232 through 235' Processing helix chain '1' and resid 239 through 244 Processing helix chain '1' and resid 261 through 267 Processing helix chain '1' and resid 276 through 299 removed outlier: 3.677A pdb=" N ALA 1 284 " --> pdb=" O HIS 1 280 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER 1 292 " --> pdb=" O LYS 1 288 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG 1 293 " --> pdb=" O THR 1 289 " (cutoff:3.500A) Processing helix chain '1' and resid 350 through 361 removed outlier: 3.523A pdb=" N ASN 1 354 " --> pdb=" O PRO 1 350 " (cutoff:3.500A) Proline residue: 1 356 - end of helix removed outlier: 3.796A pdb=" N GLY 1 359 " --> pdb=" O ILE 1 355 " (cutoff:3.500A) Proline residue: 1 360 - end of helix Processing helix chain '1' and resid 367 through 377 Proline residue: 1 371 - end of helix removed outlier: 3.562A pdb=" N ARG 1 375 " --> pdb=" O HIS 1 372 " (cutoff:3.500A) Processing helix chain '1' and resid 381 through 385 Processing helix chain '2' and resid 59 through 66 Processing helix chain '2' and resid 68 through 76 removed outlier: 4.965A pdb=" N GLU 2 73 " --> pdb=" O ASP 2 69 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR 2 76 " --> pdb=" O ALA 2 72 " (cutoff:3.500A) Processing helix chain '2' and resid 110 through 122 removed outlier: 4.077A pdb=" N GLU 2 121 " --> pdb=" O LYS 2 117 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 134 Processing helix chain '2' and resid 137 through 141 Processing helix chain '2' and resid 158 through 161 No H-bonds generated for 'chain '2' and resid 158 through 161' Processing helix chain '2' and resid 175 through 186 Processing helix chain '2' and resid 192 through 201 Proline residue: 2 195 - end of helix Processing helix chain '2' and resid 208 through 213 Processing helix chain '2' and resid 225 through 228 No H-bonds generated for 'chain '2' and resid 225 through 228' Processing helix chain '2' and resid 246 through 248 No H-bonds generated for 'chain '2' and resid 246 through 248' Processing helix chain '2' and resid 254 through 258 Processing helix chain '2' and resid 267 through 272 removed outlier: 3.524A pdb=" N LYS 2 271 " --> pdb=" O GLU 2 267 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 22 Processing helix chain '3' and resid 28 through 39 Processing helix chain '3' and resid 65 through 71 Processing helix chain '3' and resid 81 through 90 removed outlier: 3.804A pdb=" N LYS 3 86 " --> pdb=" O MET 3 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL 3 89 " --> pdb=" O LYS 3 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG 3 90 " --> pdb=" O LYS 3 87 " (cutoff:3.500A) Processing helix chain '3' and resid 103 through 114 removed outlier: 3.910A pdb=" N LYS 3 111 " --> pdb=" O MET 3 107 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET 3 112 " --> pdb=" O GLY 3 108 " (cutoff:3.500A) Processing helix chain '3' and resid 122 through 125 No H-bonds generated for 'chain '3' and resid 122 through 125' Processing helix chain '3' and resid 140 through 148 removed outlier: 3.768A pdb=" N PHE 3 146 " --> pdb=" O SER 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 181 through 184 Processing helix chain '3' and resid 190 through 194 removed outlier: 3.507A pdb=" N ILE 3 194 " --> pdb=" O GLY 3 191 " (cutoff:3.500A) Processing helix chain '3' and resid 224 through 236 Processing helix chain '3' and resid 251 through 274 removed outlier: 3.615A pdb=" N LYS 3 267 " --> pdb=" O GLU 3 263 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 47 Processing helix chain '4' and resid 52 through 62 Proline residue: 4 56 - end of helix removed outlier: 3.976A pdb=" N ARG 4 61 " --> pdb=" O VAL 4 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE 4 62 " --> pdb=" O MET 4 58 " (cutoff:3.500A) Processing helix chain '4' and resid 67 through 82 Processing helix chain '4' and resid 88 through 117 Proline residue: 4 115 - end of helix Processing helix chain '4' and resid 120 through 145 removed outlier: 3.981A pdb=" N ALA 4 124 " --> pdb=" O GLU 4 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP 4 125 " --> pdb=" O ASN 4 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR 4 139 " --> pdb=" O LYS 4 135 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL 4 140 " --> pdb=" O ASN 4 136 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 196 removed outlier: 3.688A pdb=" N ARG 4 174 " --> pdb=" O ARG 4 170 " (cutoff:3.500A) Proline residue: 4 180 - end of helix removed outlier: 3.511A pdb=" N GLU 4 187 " --> pdb=" O ASN 4 183 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU 4 194 " --> pdb=" O ILE 4 190 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP 4 195 " --> pdb=" O GLY 4 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS 4 196 " --> pdb=" O LEU 4 192 " (cutoff:3.500A) Processing helix chain '4' and resid 232 through 235 No H-bonds generated for 'chain '4' and resid 232 through 235' Processing helix chain '4' and resid 239 through 244 Processing helix chain '4' and resid 261 through 267 Processing helix chain '4' and resid 276 through 299 removed outlier: 3.677A pdb=" N ALA 4 284 " --> pdb=" O HIS 4 280 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER 4 292 " --> pdb=" O LYS 4 288 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG 4 293 " --> pdb=" O THR 4 289 " (cutoff:3.500A) Processing helix chain '4' and resid 350 through 361 removed outlier: 3.524A pdb=" N ASN 4 354 " --> pdb=" O PRO 4 350 " (cutoff:3.500A) Proline residue: 4 356 - end of helix removed outlier: 3.796A pdb=" N GLY 4 359 " --> pdb=" O ILE 4 355 " (cutoff:3.500A) Proline residue: 4 360 - end of helix Processing helix chain '4' and resid 367 through 377 Proline residue: 4 371 - end of helix removed outlier: 3.562A pdb=" N ARG 4 375 " --> pdb=" O HIS 4 372 " (cutoff:3.500A) Processing helix chain '4' and resid 381 through 385 Processing helix chain '5' and resid 59 through 66 Processing helix chain '5' and resid 68 through 76 removed outlier: 4.966A pdb=" N GLU 5 73 " --> pdb=" O ASP 5 69 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR 5 76 " --> pdb=" O ALA 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 110 through 122 removed outlier: 4.076A pdb=" N GLU 5 121 " --> pdb=" O LYS 5 117 " (cutoff:3.500A) Processing helix chain '5' and resid 130 through 134 Processing helix chain '5' and resid 137 through 141 Processing helix chain '5' and resid 158 through 161 No H-bonds generated for 'chain '5' and resid 158 through 161' Processing helix chain '5' and resid 175 through 186 Processing helix chain '5' and resid 192 through 201 Proline residue: 5 195 - end of helix Processing helix chain '5' and resid 208 through 213 Processing helix chain '5' and resid 225 through 228 No H-bonds generated for 'chain '5' and resid 225 through 228' Processing helix chain '5' and resid 246 through 248 No H-bonds generated for 'chain '5' and resid 246 through 248' Processing helix chain '5' and resid 254 through 258 Processing helix chain '5' and resid 267 through 272 removed outlier: 3.524A pdb=" N LYS 5 271 " --> pdb=" O GLU 5 267 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 22 Processing helix chain '6' and resid 28 through 39 Processing helix chain '6' and resid 65 through 71 Processing helix chain '6' and resid 81 through 90 removed outlier: 3.804A pdb=" N LYS 6 86 " --> pdb=" O MET 6 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL 6 89 " --> pdb=" O LYS 6 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG 6 90 " --> pdb=" O LYS 6 87 " (cutoff:3.500A) Processing helix chain '6' and resid 103 through 114 removed outlier: 3.910A pdb=" N LYS 6 111 " --> pdb=" O MET 6 107 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET 6 112 " --> pdb=" O GLY 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 125 No H-bonds generated for 'chain '6' and resid 122 through 125' Processing helix chain '6' and resid 140 through 148 removed outlier: 3.769A pdb=" N PHE 6 146 " --> pdb=" O SER 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 181 through 184 Processing helix chain '6' and resid 190 through 194 removed outlier: 3.507A pdb=" N ILE 6 194 " --> pdb=" O GLY 6 191 " (cutoff:3.500A) Processing helix chain '6' and resid 224 through 236 Processing helix chain '6' and resid 251 through 274 removed outlier: 3.616A pdb=" N LYS 6 267 " --> pdb=" O GLU 6 263 " (cutoff:3.500A) Processing helix chain '7' and resid 43 through 47 Processing helix chain '7' and resid 52 through 62 Proline residue: 7 56 - end of helix removed outlier: 3.975A pdb=" N ARG 7 61 " --> pdb=" O VAL 7 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE 7 62 " --> pdb=" O MET 7 58 " (cutoff:3.500A) Processing helix chain '7' and resid 67 through 82 Processing helix chain '7' and resid 88 through 117 Proline residue: 7 115 - end of helix Processing helix chain '7' and resid 120 through 145 removed outlier: 3.982A pdb=" N ALA 7 124 " --> pdb=" O GLU 7 120 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP 7 125 " --> pdb=" O ASN 7 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR 7 139 " --> pdb=" O LYS 7 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL 7 140 " --> pdb=" O ASN 7 136 " (cutoff:3.500A) Processing helix chain '7' and resid 165 through 196 removed outlier: 3.689A pdb=" N ARG 7 174 " --> pdb=" O ARG 7 170 " (cutoff:3.500A) Proline residue: 7 180 - end of helix removed outlier: 3.512A pdb=" N GLU 7 187 " --> pdb=" O ASN 7 183 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU 7 194 " --> pdb=" O ILE 7 190 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP 7 195 " --> pdb=" O GLY 7 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS 7 196 " --> pdb=" O LEU 7 192 " (cutoff:3.500A) Processing helix chain '7' and resid 232 through 235 No H-bonds generated for 'chain '7' and resid 232 through 235' Processing helix chain '7' and resid 239 through 244 Processing helix chain '7' and resid 261 through 267 Processing helix chain '7' and resid 276 through 299 removed outlier: 3.678A pdb=" N ALA 7 284 " --> pdb=" O HIS 7 280 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER 7 292 " --> pdb=" O LYS 7 288 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG 7 293 " --> pdb=" O THR 7 289 " (cutoff:3.500A) Processing helix chain '7' and resid 350 through 361 removed outlier: 3.523A pdb=" N ASN 7 354 " --> pdb=" O PRO 7 350 " (cutoff:3.500A) Proline residue: 7 356 - end of helix removed outlier: 3.797A pdb=" N GLY 7 359 " --> pdb=" O ILE 7 355 " (cutoff:3.500A) Proline residue: 7 360 - end of helix Processing helix chain '7' and resid 367 through 377 Proline residue: 7 371 - end of helix removed outlier: 3.562A pdb=" N ARG 7 375 " --> pdb=" O HIS 7 372 " (cutoff:3.500A) Processing helix chain '7' and resid 381 through 385 Processing helix chain '8' and resid 59 through 66 Processing helix chain '8' and resid 68 through 76 removed outlier: 4.966A pdb=" N GLU 8 73 " --> pdb=" O ASP 8 69 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) Processing helix chain '8' and resid 110 through 122 removed outlier: 4.076A pdb=" N GLU 8 121 " --> pdb=" O LYS 8 117 " (cutoff:3.500A) Processing helix chain '8' and resid 130 through 134 Processing helix chain '8' and resid 137 through 141 Processing helix chain '8' and resid 158 through 161 No H-bonds generated for 'chain '8' and resid 158 through 161' Processing helix chain '8' and resid 175 through 186 Processing helix chain '8' and resid 192 through 201 Proline residue: 8 195 - end of helix Processing helix chain '8' and resid 208 through 213 Processing helix chain '8' and resid 225 through 228 No H-bonds generated for 'chain '8' and resid 225 through 228' Processing helix chain '8' and resid 246 through 248 No H-bonds generated for 'chain '8' and resid 246 through 248' Processing helix chain '8' and resid 254 through 258 Processing helix chain '8' and resid 267 through 272 removed outlier: 3.524A pdb=" N LYS 8 271 " --> pdb=" O GLU 8 267 " (cutoff:3.500A) Processing helix chain '9' and resid 17 through 22 Processing helix chain '9' and resid 28 through 39 Processing helix chain '9' and resid 65 through 71 Processing helix chain '9' and resid 81 through 90 removed outlier: 3.805A pdb=" N LYS 9 86 " --> pdb=" O MET 9 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL 9 89 " --> pdb=" O LYS 9 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG 9 90 " --> pdb=" O LYS 9 87 " (cutoff:3.500A) Processing helix chain '9' and resid 103 through 114 removed outlier: 3.911A pdb=" N LYS 9 111 " --> pdb=" O MET 9 107 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET 9 112 " --> pdb=" O GLY 9 108 " (cutoff:3.500A) Processing helix chain '9' and resid 122 through 125 No H-bonds generated for 'chain '9' and resid 122 through 125' Processing helix chain '9' and resid 140 through 148 removed outlier: 3.768A pdb=" N PHE 9 146 " --> pdb=" O SER 9 142 " (cutoff:3.500A) Processing helix chain '9' and resid 181 through 184 Processing helix chain '9' and resid 190 through 194 removed outlier: 3.506A pdb=" N ILE 9 194 " --> pdb=" O GLY 9 191 " (cutoff:3.500A) Processing helix chain '9' and resid 224 through 236 Processing helix chain '9' and resid 251 through 274 removed outlier: 3.616A pdb=" N LYS 9 267 " --> pdb=" O GLU 9 263 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.763A pdb=" N GLU A 3 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS A 31 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 227 through 230 Processing sheet with id= C, first strand: chain 'A' and resid 319 through 326 removed outlier: 3.874A pdb=" N PHE A 344 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU A 338 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 49 through 52 removed outlier: 6.015A pdb=" N LEU B 98 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE B 52 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU B 100 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU B 125 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL B 101 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS B 127 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU B 166 " --> pdb=" O ALA B 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 235 through 237 Processing sheet with id= F, first strand: chain 'C' and resid 239 through 243 removed outlier: 3.807A pdb=" N GLU C 8 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C 205 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL C 130 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR C 99 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE C 132 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA C 101 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY C 44 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL C 100 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C 46 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE C 102 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ALA C 48 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 45 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 175 through 179 Processing sheet with id= H, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.764A pdb=" N GLU D 3 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 31 " --> pdb=" O GLU D 22 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 227 through 230 Processing sheet with id= J, first strand: chain 'D' and resid 319 through 326 removed outlier: 3.874A pdb=" N PHE D 344 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU D 338 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE D 342 " --> pdb=" O GLU D 338 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.014A pdb=" N LEU E 98 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE E 52 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU E 100 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU E 125 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL E 101 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS E 127 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU E 166 " --> pdb=" O ALA E 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 235 through 237 Processing sheet with id= M, first strand: chain 'F' and resid 239 through 243 removed outlier: 3.807A pdb=" N GLU F 8 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL F 205 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL F 130 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR F 99 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE F 132 " --> pdb=" O THR F 99 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA F 101 " --> pdb=" O ILE F 132 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY F 44 " --> pdb=" O GLY F 98 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL F 100 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL F 46 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ILE F 102 " --> pdb=" O VAL F 46 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ALA F 48 " --> pdb=" O ILE F 102 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA F 45 " --> pdb=" O ALA F 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 175 through 179 Processing sheet with id= O, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.763A pdb=" N GLU G 3 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS G 31 " --> pdb=" O GLU G 22 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 227 through 230 Processing sheet with id= Q, first strand: chain 'G' and resid 319 through 326 removed outlier: 3.874A pdb=" N PHE G 344 " --> pdb=" O LYS G 336 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU G 338 " --> pdb=" O ILE G 342 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE G 342 " --> pdb=" O GLU G 338 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 49 through 52 removed outlier: 6.015A pdb=" N LEU H 98 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE H 52 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU H 100 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU H 125 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL H 101 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS H 127 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU H 166 " --> pdb=" O ALA H 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'H' and resid 235 through 237 Processing sheet with id= T, first strand: chain 'I' and resid 239 through 243 removed outlier: 3.806A pdb=" N GLU I 8 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL I 205 " --> pdb=" O LEU I 129 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL I 130 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR I 99 " --> pdb=" O VAL I 130 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE I 132 " --> pdb=" O THR I 99 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA I 101 " --> pdb=" O ILE I 132 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY I 44 " --> pdb=" O GLY I 98 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL I 100 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL I 46 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE I 102 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ALA I 48 " --> pdb=" O ILE I 102 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA I 45 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 175 through 179 Processing sheet with id= V, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.764A pdb=" N GLU J 3 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS J 31 " --> pdb=" O GLU J 22 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 227 through 230 Processing sheet with id= X, first strand: chain 'J' and resid 319 through 326 removed outlier: 3.874A pdb=" N PHE J 344 " --> pdb=" O LYS J 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU J 338 " --> pdb=" O ILE J 342 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE J 342 " --> pdb=" O GLU J 338 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 49 through 52 removed outlier: 6.015A pdb=" N LEU K 98 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE K 52 " --> pdb=" O LEU K 98 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU K 100 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU K 125 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL K 101 " --> pdb=" O LEU K 125 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS K 127 " --> pdb=" O VAL K 101 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU K 166 " --> pdb=" O ALA K 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'K' and resid 235 through 237 Processing sheet with id= AA, first strand: chain 'L' and resid 239 through 243 removed outlier: 3.807A pdb=" N GLU L 8 " --> pdb=" O THR L 221 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL L 205 " --> pdb=" O LEU L 129 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL L 130 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR L 99 " --> pdb=" O VAL L 130 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE L 132 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA L 101 " --> pdb=" O ILE L 132 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY L 44 " --> pdb=" O GLY L 98 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL L 100 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL L 46 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE L 102 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ALA L 48 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA L 45 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 175 through 179 Processing sheet with id= AC, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.763A pdb=" N GLU M 3 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS M 31 " --> pdb=" O GLU M 22 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 227 through 230 Processing sheet with id= AE, first strand: chain 'M' and resid 319 through 326 removed outlier: 3.874A pdb=" N PHE M 344 " --> pdb=" O LYS M 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU M 338 " --> pdb=" O ILE M 342 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE M 342 " --> pdb=" O GLU M 338 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 49 through 52 removed outlier: 6.015A pdb=" N LEU N 98 " --> pdb=" O GLY N 50 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE N 52 " --> pdb=" O LEU N 98 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU N 100 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU N 125 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL N 101 " --> pdb=" O LEU N 125 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS N 127 " --> pdb=" O VAL N 101 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU N 166 " --> pdb=" O ALA N 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'N' and resid 235 through 237 Processing sheet with id= AH, first strand: chain 'O' and resid 239 through 243 removed outlier: 3.806A pdb=" N GLU O 8 " --> pdb=" O THR O 221 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL O 205 " --> pdb=" O LEU O 129 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL O 130 " --> pdb=" O LEU O 97 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR O 99 " --> pdb=" O VAL O 130 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE O 132 " --> pdb=" O THR O 99 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA O 101 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY O 44 " --> pdb=" O GLY O 98 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL O 100 " --> pdb=" O GLY O 44 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL O 46 " --> pdb=" O VAL O 100 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE O 102 " --> pdb=" O VAL O 46 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ALA O 48 " --> pdb=" O ILE O 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA O 45 " --> pdb=" O ALA O 62 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'O' and resid 175 through 179 Processing sheet with id= AJ, first strand: chain 'P' and resid 3 through 7 removed outlier: 3.763A pdb=" N GLU P 3 " --> pdb=" O VAL P 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS P 31 " --> pdb=" O GLU P 22 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'P' and resid 227 through 230 Processing sheet with id= AL, first strand: chain 'P' and resid 319 through 326 removed outlier: 3.874A pdb=" N PHE P 344 " --> pdb=" O LYS P 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU P 338 " --> pdb=" O ILE P 342 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE P 342 " --> pdb=" O GLU P 338 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'Q' and resid 49 through 52 removed outlier: 6.015A pdb=" N LEU Q 98 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE Q 52 " --> pdb=" O LEU Q 98 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU Q 100 " --> pdb=" O ILE Q 52 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU Q 125 " --> pdb=" O ALA Q 99 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL Q 101 " --> pdb=" O LEU Q 125 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N CYS Q 127 " --> pdb=" O VAL Q 101 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU Q 166 " --> pdb=" O ALA Q 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'Q' and resid 235 through 237 Processing sheet with id= AO, first strand: chain 'R' and resid 239 through 243 removed outlier: 3.806A pdb=" N GLU R 8 " --> pdb=" O THR R 221 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL R 205 " --> pdb=" O LEU R 129 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL R 130 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR R 99 " --> pdb=" O VAL R 130 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE R 132 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA R 101 " --> pdb=" O ILE R 132 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY R 44 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL R 100 " --> pdb=" O GLY R 44 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL R 46 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE R 102 " --> pdb=" O VAL R 46 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ALA R 48 " --> pdb=" O ILE R 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA R 45 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'R' and resid 175 through 179 Processing sheet with id= AQ, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.763A pdb=" N GLU S 3 " --> pdb=" O VAL S 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS S 31 " --> pdb=" O GLU S 22 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'S' and resid 227 through 230 Processing sheet with id= AS, first strand: chain 'S' and resid 319 through 326 removed outlier: 3.874A pdb=" N PHE S 344 " --> pdb=" O LYS S 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU S 338 " --> pdb=" O ILE S 342 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE S 342 " --> pdb=" O GLU S 338 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'T' and resid 49 through 52 removed outlier: 6.016A pdb=" N LEU T 98 " --> pdb=" O GLY T 50 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE T 52 " --> pdb=" O LEU T 98 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU T 100 " --> pdb=" O ILE T 52 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU T 125 " --> pdb=" O ALA T 99 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL T 101 " --> pdb=" O LEU T 125 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N CYS T 127 " --> pdb=" O VAL T 101 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU T 166 " --> pdb=" O ALA T 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'T' and resid 235 through 237 Processing sheet with id= AV, first strand: chain 'U' and resid 239 through 243 removed outlier: 3.806A pdb=" N GLU U 8 " --> pdb=" O THR U 221 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL U 205 " --> pdb=" O LEU U 129 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL U 130 " --> pdb=" O LEU U 97 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR U 99 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE U 132 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA U 101 " --> pdb=" O ILE U 132 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY U 44 " --> pdb=" O GLY U 98 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL U 100 " --> pdb=" O GLY U 44 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL U 46 " --> pdb=" O VAL U 100 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ILE U 102 " --> pdb=" O VAL U 46 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ALA U 48 " --> pdb=" O ILE U 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA U 45 " --> pdb=" O ALA U 62 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'U' and resid 175 through 179 Processing sheet with id= AX, first strand: chain 'V' and resid 3 through 7 removed outlier: 3.763A pdb=" N GLU V 3 " --> pdb=" O VAL V 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS V 31 " --> pdb=" O GLU V 22 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'V' and resid 227 through 230 Processing sheet with id= AZ, first strand: chain 'V' and resid 319 through 326 removed outlier: 3.874A pdb=" N PHE V 344 " --> pdb=" O LYS V 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU V 338 " --> pdb=" O ILE V 342 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE V 342 " --> pdb=" O GLU V 338 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'W' and resid 49 through 52 removed outlier: 6.016A pdb=" N LEU W 98 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE W 52 " --> pdb=" O LEU W 98 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU W 100 " --> pdb=" O ILE W 52 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU W 125 " --> pdb=" O ALA W 99 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL W 101 " --> pdb=" O LEU W 125 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS W 127 " --> pdb=" O VAL W 101 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU W 166 " --> pdb=" O ALA W 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'W' and resid 235 through 237 Processing sheet with id= BC, first strand: chain 'X' and resid 239 through 243 removed outlier: 3.806A pdb=" N GLU X 8 " --> pdb=" O THR X 221 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL X 205 " --> pdb=" O LEU X 129 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL X 130 " --> pdb=" O LEU X 97 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR X 99 " --> pdb=" O VAL X 130 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE X 132 " --> pdb=" O THR X 99 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA X 101 " --> pdb=" O ILE X 132 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY X 44 " --> pdb=" O GLY X 98 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL X 100 " --> pdb=" O GLY X 44 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL X 46 " --> pdb=" O VAL X 100 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE X 102 " --> pdb=" O VAL X 46 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ALA X 48 " --> pdb=" O ILE X 102 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA X 45 " --> pdb=" O ALA X 62 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'X' and resid 175 through 179 Processing sheet with id= BE, first strand: chain 'Y' and resid 3 through 7 removed outlier: 3.762A pdb=" N GLU Y 3 " --> pdb=" O VAL Y 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS Y 31 " --> pdb=" O GLU Y 22 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'Y' and resid 227 through 230 Processing sheet with id= BG, first strand: chain 'Y' and resid 319 through 326 removed outlier: 3.875A pdb=" N PHE Y 344 " --> pdb=" O LYS Y 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU Y 338 " --> pdb=" O ILE Y 342 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE Y 342 " --> pdb=" O GLU Y 338 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'Z' and resid 49 through 52 removed outlier: 6.016A pdb=" N LEU Z 98 " --> pdb=" O GLY Z 50 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE Z 52 " --> pdb=" O LEU Z 98 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU Z 100 " --> pdb=" O ILE Z 52 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU Z 125 " --> pdb=" O ALA Z 99 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL Z 101 " --> pdb=" O LEU Z 125 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS Z 127 " --> pdb=" O VAL Z 101 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU Z 166 " --> pdb=" O ALA Z 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'Z' and resid 235 through 237 Processing sheet with id= BJ, first strand: chain '0' and resid 239 through 243 removed outlier: 3.807A pdb=" N GLU 0 8 " --> pdb=" O THR 0 221 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL 0 205 " --> pdb=" O LEU 0 129 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL 0 130 " --> pdb=" O LEU 0 97 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR 0 99 " --> pdb=" O VAL 0 130 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE 0 132 " --> pdb=" O THR 0 99 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA 0 101 " --> pdb=" O ILE 0 132 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY 0 44 " --> pdb=" O GLY 0 98 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL 0 100 " --> pdb=" O GLY 0 44 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL 0 46 " --> pdb=" O VAL 0 100 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE 0 102 " --> pdb=" O VAL 0 46 " (cutoff:3.500A) removed outlier: 11.269A pdb=" N ALA 0 48 " --> pdb=" O ILE 0 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA 0 45 " --> pdb=" O ALA 0 62 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain '0' and resid 175 through 179 Processing sheet with id= BL, first strand: chain '1' and resid 3 through 7 removed outlier: 3.762A pdb=" N GLU 1 3 " --> pdb=" O VAL 1 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS 1 31 " --> pdb=" O GLU 1 22 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain '1' and resid 227 through 230 Processing sheet with id= BN, first strand: chain '1' and resid 319 through 326 removed outlier: 3.874A pdb=" N PHE 1 344 " --> pdb=" O LYS 1 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU 1 338 " --> pdb=" O ILE 1 342 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE 1 342 " --> pdb=" O GLU 1 338 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain '2' and resid 49 through 52 removed outlier: 6.016A pdb=" N LEU 2 98 " --> pdb=" O GLY 2 50 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE 2 52 " --> pdb=" O LEU 2 98 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU 2 100 " --> pdb=" O ILE 2 52 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU 2 125 " --> pdb=" O ALA 2 99 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL 2 101 " --> pdb=" O LEU 2 125 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS 2 127 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU 2 166 " --> pdb=" O ALA 2 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= BO Processing sheet with id= BP, first strand: chain '2' and resid 235 through 237 Processing sheet with id= BQ, first strand: chain '3' and resid 239 through 243 removed outlier: 3.807A pdb=" N GLU 3 8 " --> pdb=" O THR 3 221 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL 3 205 " --> pdb=" O LEU 3 129 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL 3 130 " --> pdb=" O LEU 3 97 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR 3 99 " --> pdb=" O VAL 3 130 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE 3 132 " --> pdb=" O THR 3 99 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA 3 101 " --> pdb=" O ILE 3 132 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY 3 44 " --> pdb=" O GLY 3 98 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL 3 100 " --> pdb=" O GLY 3 44 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL 3 46 " --> pdb=" O VAL 3 100 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE 3 102 " --> pdb=" O VAL 3 46 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ALA 3 48 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA 3 45 " --> pdb=" O ALA 3 62 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain '3' and resid 175 through 179 Processing sheet with id= BS, first strand: chain '4' and resid 3 through 7 removed outlier: 3.763A pdb=" N GLU 4 3 " --> pdb=" O VAL 4 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS 4 31 " --> pdb=" O GLU 4 22 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain '4' and resid 227 through 230 Processing sheet with id= BU, first strand: chain '4' and resid 319 through 326 removed outlier: 3.874A pdb=" N PHE 4 344 " --> pdb=" O LYS 4 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU 4 338 " --> pdb=" O ILE 4 342 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE 4 342 " --> pdb=" O GLU 4 338 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain '5' and resid 49 through 52 removed outlier: 6.016A pdb=" N LEU 5 98 " --> pdb=" O GLY 5 50 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE 5 52 " --> pdb=" O LEU 5 98 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU 5 100 " --> pdb=" O ILE 5 52 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU 5 125 " --> pdb=" O ALA 5 99 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL 5 101 " --> pdb=" O LEU 5 125 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS 5 127 " --> pdb=" O VAL 5 101 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU 5 166 " --> pdb=" O ALA 5 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain '5' and resid 235 through 237 Processing sheet with id= BX, first strand: chain '6' and resid 239 through 243 removed outlier: 3.807A pdb=" N GLU 6 8 " --> pdb=" O THR 6 221 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL 6 205 " --> pdb=" O LEU 6 129 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL 6 130 " --> pdb=" O LEU 6 97 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR 6 99 " --> pdb=" O VAL 6 130 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE 6 132 " --> pdb=" O THR 6 99 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA 6 101 " --> pdb=" O ILE 6 132 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY 6 44 " --> pdb=" O GLY 6 98 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL 6 100 " --> pdb=" O GLY 6 44 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL 6 46 " --> pdb=" O VAL 6 100 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE 6 102 " --> pdb=" O VAL 6 46 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ALA 6 48 " --> pdb=" O ILE 6 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA 6 45 " --> pdb=" O ALA 6 62 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain '6' and resid 175 through 179 Processing sheet with id= BZ, first strand: chain '7' and resid 3 through 7 removed outlier: 3.763A pdb=" N GLU 7 3 " --> pdb=" O VAL 7 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS 7 31 " --> pdb=" O GLU 7 22 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain '7' and resid 227 through 230 Processing sheet with id= CB, first strand: chain '7' and resid 319 through 326 removed outlier: 3.874A pdb=" N PHE 7 344 " --> pdb=" O LYS 7 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU 7 338 " --> pdb=" O ILE 7 342 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE 7 342 " --> pdb=" O GLU 7 338 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain '8' and resid 49 through 52 removed outlier: 6.015A pdb=" N LEU 8 98 " --> pdb=" O GLY 8 50 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE 8 52 " --> pdb=" O LEU 8 98 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU 8 100 " --> pdb=" O ILE 8 52 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU 8 125 " --> pdb=" O ALA 8 99 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL 8 101 " --> pdb=" O LEU 8 125 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS 8 127 " --> pdb=" O VAL 8 101 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU 8 166 " --> pdb=" O ALA 8 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= CC Processing sheet with id= CD, first strand: chain '8' and resid 235 through 237 Processing sheet with id= CE, first strand: chain '9' and resid 239 through 243 removed outlier: 3.806A pdb=" N GLU 9 8 " --> pdb=" O THR 9 221 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL 9 205 " --> pdb=" O LEU 9 129 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL 9 130 " --> pdb=" O LEU 9 97 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR 9 99 " --> pdb=" O VAL 9 130 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE 9 132 " --> pdb=" O THR 9 99 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA 9 101 " --> pdb=" O ILE 9 132 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY 9 44 " --> pdb=" O GLY 9 98 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL 9 100 " --> pdb=" O GLY 9 44 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL 9 46 " --> pdb=" O VAL 9 100 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE 9 102 " --> pdb=" O VAL 9 46 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ALA 9 48 " --> pdb=" O ILE 9 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA 9 45 " --> pdb=" O ALA 9 62 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain '9' and resid 175 through 179 3024 hydrogen bonds defined for protein. 8316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 35.52 Time building geometry restraints manager: 28.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.41: 33254 1.41 - 1.64: 50410 1.64 - 1.87: 1020 1.87 - 2.10: 12 2.10 - 2.33: 576 Bond restraints: 85272 Sorted by residual: bond pdb=" C ARG K 241 " pdb=" N PRO K 242 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.11e-02 8.12e+03 4.03e+01 bond pdb=" C ARG E 241 " pdb=" N PRO E 242 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.11e-02 8.12e+03 4.03e+01 bond pdb=" C ARG H 241 " pdb=" N PRO H 242 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.11e-02 8.12e+03 4.03e+01 bond pdb=" C ARG 5 241 " pdb=" N PRO 5 242 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.11e-02 8.12e+03 4.00e+01 bond pdb=" C ARG N 241 " pdb=" N PRO N 242 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.11e-02 8.12e+03 3.99e+01 ... (remaining 85267 not shown) Histogram of bond angle deviations from ideal: 70.68 - 84.76: 576 84.76 - 98.83: 0 98.83 - 112.90: 47491 112.90 - 126.98: 66870 126.98 - 141.05: 1055 Bond angle restraints: 115992 Sorted by residual: angle pdb=" N GLY 8 130 " pdb=" CA GLY 8 130 " pdb=" C GLY 8 130 " ideal model delta sigma weight residual 112.48 99.62 12.86 1.21e+00 6.83e-01 1.13e+02 angle pdb=" N GLY H 130 " pdb=" CA GLY H 130 " pdb=" C GLY H 130 " ideal model delta sigma weight residual 112.48 99.63 12.85 1.21e+00 6.83e-01 1.13e+02 angle pdb=" N GLY N 130 " pdb=" CA GLY N 130 " pdb=" C GLY N 130 " ideal model delta sigma weight residual 112.48 99.64 12.84 1.21e+00 6.83e-01 1.13e+02 angle pdb=" N GLY B 130 " pdb=" CA GLY B 130 " pdb=" C GLY B 130 " ideal model delta sigma weight residual 112.48 99.66 12.82 1.21e+00 6.83e-01 1.12e+02 angle pdb=" N GLY 5 130 " pdb=" CA GLY 5 130 " pdb=" C GLY 5 130 " ideal model delta sigma weight residual 112.48 99.66 12.82 1.21e+00 6.83e-01 1.12e+02 ... (remaining 115987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.66: 45971 32.66 - 65.33: 5545 65.33 - 97.99: 264 97.99 - 130.66: 0 130.66 - 163.32: 12 Dihedral angle restraints: 51792 sinusoidal: 21120 harmonic: 30672 Sorted by residual: dihedral pdb=" CD ARG 0 272 " pdb=" NE ARG 0 272 " pdb=" CZ ARG 0 272 " pdb=" NH1 ARG 0 272 " ideal model delta sinusoidal sigma weight residual 0.00 -88.25 88.25 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CD ARG R 272 " pdb=" NE ARG R 272 " pdb=" CZ ARG R 272 " pdb=" NH1 ARG R 272 " ideal model delta sinusoidal sigma weight residual 0.00 -88.24 88.24 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CD ARG 3 272 " pdb=" NE ARG 3 272 " pdb=" CZ ARG 3 272 " pdb=" NH1 ARG 3 272 " ideal model delta sinusoidal sigma weight residual 0.00 -88.23 88.23 1 1.00e+01 1.00e-02 9.30e+01 ... (remaining 51789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.262: 13068 4.262 - 8.523: 0 8.523 - 12.785: 0 12.785 - 17.047: 0 17.047 - 21.309: 96 Chirality restraints: 13164 Sorted by residual: chirality pdb="FE3 SF4 51275 " pdb=" S1 SF4 51275 " pdb=" S2 SF4 51275 " pdb=" S4 SF4 51275 " both_signs ideal model delta sigma weight residual False -10.55 10.75 -21.31 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE3 SF4 N1275 " pdb=" S1 SF4 N1275 " pdb=" S2 SF4 N1275 " pdb=" S4 SF4 N1275 " both_signs ideal model delta sigma weight residual False -10.55 10.75 -21.31 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE3 SF4 W1275 " pdb=" S1 SF4 W1275 " pdb=" S2 SF4 W1275 " pdb=" S4 SF4 W1275 " both_signs ideal model delta sigma weight residual False -10.55 10.75 -21.31 2.00e-01 2.50e+01 1.14e+04 ... (remaining 13161 not shown) Planarity restraints: 14808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 272 " 1.104 9.50e-02 1.11e+02 4.95e-01 1.47e+02 pdb=" NE ARG I 272 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG I 272 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG I 272 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG I 272 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 9 272 " -1.104 9.50e-02 1.11e+02 4.95e-01 1.47e+02 pdb=" NE ARG 9 272 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG 9 272 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG 9 272 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG 9 272 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 272 " -1.104 9.50e-02 1.11e+02 4.95e-01 1.47e+02 pdb=" NE ARG F 272 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG F 272 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG F 272 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG F 272 " -0.016 2.00e-02 2.50e+03 ... (remaining 14805 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 2079 2.51 - 3.11: 76371 3.11 - 3.71: 135960 3.71 - 4.30: 201844 4.30 - 4.90: 331211 Nonbonded interactions: 747465 Sorted by model distance: nonbonded pdb=" N GLN G 214 " pdb=" OE1 GLN G 214 " model vdw 1.915 2.520 nonbonded pdb=" N GLN M 214 " pdb=" OE1 GLN M 214 " model vdw 1.915 2.520 nonbonded pdb=" N GLN V 214 " pdb=" OE1 GLN V 214 " model vdw 1.915 2.520 nonbonded pdb=" N GLN A 214 " pdb=" OE1 GLN A 214 " model vdw 1.916 2.520 nonbonded pdb=" N GLN 4 214 " pdb=" OE1 GLN 4 214 " model vdw 1.916 2.520 ... (remaining 747460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '3' selection = chain '6' selection = chain '9' selection = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain '1' selection = chain '4' selection = chain '7' selection = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = chain '2' selection = chain '5' selection = chain '8' selection = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 6.400 Check model and map are aligned: 0.940 Set scattering table: 0.570 Process input model: 201.160 Find NCS groups from input model: 4.400 Set up NCS constraints: 0.810 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 217.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.160 85272 Z= 0.956 Angle : 1.935 19.120 115992 Z= 1.246 Chirality : 1.740 21.309 13164 Planarity : 0.030 0.495 14808 Dihedral : 23.870 163.320 32112 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 119.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Rotamer: Outliers : 39.11 % Allowed : 19.01 % Favored : 41.88 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.08), residues: 10644 helix: 2.35 (0.07), residues: 4056 sheet: 1.13 (0.12), residues: 1716 loop : 0.26 (0.09), residues: 4872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 2 91 HIS 0.008 0.002 HIS D 101 PHE 0.012 0.002 PHE D 268 TYR 0.021 0.003 TYR R 35 ARG 0.004 0.000 ARG 9 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6587 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3492 poor density : 3095 time to evaluate : 7.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3492 outliers final: 926 residues processed: 5289 average time/residue: 0.8772 time to fit residues: 7684.2860 Evaluate side-chains 2889 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 926 poor density : 1963 time to evaluate : 7.068 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 926 outliers final: 16 residues processed: 926 average time/residue: 0.7395 time to fit residues: 1227.0817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 891 optimal weight: 7.9990 chunk 800 optimal weight: 5.9990 chunk 444 optimal weight: 0.8980 chunk 273 optimal weight: 10.0000 chunk 539 optimal weight: 6.9990 chunk 427 optimal weight: 4.9990 chunk 827 optimal weight: 9.9990 chunk 320 optimal weight: 0.9990 chunk 503 optimal weight: 3.9990 chunk 616 optimal weight: 9.9990 chunk 958 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS A 60 GLN A 102 HIS A 280 HIS A 343 GLN A 366 HIS B 114 HIS B 146 GLN B 188 ASN B 194 GLN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN C 91 GLN C 105 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN C 268 ASN D 206 ASN D 279 GLN D 280 HIS ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS D 372 HIS ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS E 146 GLN E 187 ASN E 216 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 HIS ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN G 16 HIS ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 HIS ** G 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 HIS H 146 GLN H 149 GLN H 152 HIS H 187 ASN H 194 GLN H 217 GLN H 258 GLN I 185 HIS ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 268 ASN J 16 HIS J 60 GLN ** J 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 HIS J 177 GLN J 185 HIS J 206 ASN J 280 HIS J 366 HIS K 146 GLN ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 105 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 268 ASN M 60 GLN ** M 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN M 138 GLN ** M 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 GLN M 280 HIS M 333 HIS ** M 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 372 HIS N 67 ASN N 114 HIS N 146 GLN ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 ASN N 217 GLN N 268 GLN O 91 GLN ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 232 GLN O 268 ASN P 60 GLN P 269 GLN P 280 HIS ** P 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 GLN Q 147 GLN Q 188 ASN Q 217 GLN ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 GLN R 105 GLN ** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 268 ASN S 16 HIS ** S 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 HIS S 128 ASN S 150 HIS ** S 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 HIS S 354 ASN S 366 HIS T 114 HIS T 146 GLN T 149 GLN T 216 ASN T 217 GLN U 91 GLN U 185 HIS ** U 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 268 ASN V 16 HIS ** V 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 102 HIS V 206 ASN V 269 GLN ** V 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 372 HIS W 114 HIS W 146 GLN ** W 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 217 GLN W 231 GLN X 91 GLN X 105 GLN ** X 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 268 ASN ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 102 HIS Y 136 ASN Y 177 GLN Y 206 ASN ** Y 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 366 HIS Z 114 HIS Z 146 GLN Z 216 ASN Z 217 GLN 0 91 GLN 0 185 HIS ** 0 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 268 ASN 1 16 HIS 1 102 HIS 1 121 ASN 1 269 GLN ** 1 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 354 ASN ** 2 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 114 HIS 2 146 GLN ** 2 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 268 ASN 4 102 HIS 4 106 HIS 4 128 ASN 4 136 ASN ** 4 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 354 ASN 4 366 HIS 4 367 HIS 4 372 HIS ** 5 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 67 ASN ** 5 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 114 HIS 5 146 GLN 5 187 ASN 5 217 GLN 5 258 GLN 6 20 GLN 6 113 GLN 6 185 HIS ** 6 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 268 ASN 7 16 HIS 7 60 GLN 7 102 HIS ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 206 ASN ** 7 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 354 ASN 7 366 HIS 8 146 GLN 8 188 ASN 8 217 GLN ** 8 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 105 GLN 9 185 HIS ** 9 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 268 ASN Total number of N/Q/H flips: 156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.263 85272 Z= 0.961 Angle : 2.790 50.856 115992 Z= 1.810 Chirality : 0.557 6.778 13164 Planarity : 0.009 0.375 14808 Dihedral : 10.913 179.557 12048 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 8.22 % Allowed : 27.31 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.08), residues: 10644 helix: 0.33 (0.07), residues: 4296 sheet: 0.60 (0.13), residues: 1560 loop : -0.52 (0.09), residues: 4788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP U 169 HIS 0.034 0.003 HIS 4 70 PHE 0.037 0.003 PHE M 35 TYR 0.038 0.003 TYR 3 133 ARG 0.029 0.001 ARG 0 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3107 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 734 poor density : 2373 time to evaluate : 7.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 734 outliers final: 311 residues processed: 2894 average time/residue: 0.8307 time to fit residues: 4171.5034 Evaluate side-chains 2052 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1741 time to evaluate : 7.124 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 311 outliers final: 1 residues processed: 311 average time/residue: 0.6347 time to fit residues: 383.6084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 532 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 chunk 798 optimal weight: 0.8980 chunk 652 optimal weight: 0.9980 chunk 264 optimal weight: 20.0000 chunk 960 optimal weight: 1.9990 chunk 1037 optimal weight: 5.9990 chunk 855 optimal weight: 1.9990 chunk 952 optimal weight: 1.9990 chunk 327 optimal weight: 0.9990 chunk 770 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 185 HIS ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN B 187 ASN B 216 ASN C 185 HIS C 189 GLN ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN E 149 GLN E 258 GLN E 268 GLN F 105 GLN F 189 GLN ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN G 206 ASN G 269 GLN G 280 HIS ** G 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 GLN I 232 GLN J 13 GLN J 177 GLN J 206 ASN K 147 GLN ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 GLN L 58 GLN L 189 GLN M 13 GLN M 136 ASN ** M 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 366 HIS M 372 HIS ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 217 GLN ** N 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 GLN P 206 ASN P 343 GLN P 366 HIS Q 67 ASN Q 147 GLN Q 194 GLN Q 216 ASN ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 GLN R 185 HIS S 13 GLN S 206 ASN S 339 ASN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 216 ASN ** T 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 GLN U 105 GLN U 189 GLN ** V 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 280 HIS ** W 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 GLN X 113 GLN X 189 GLN Y 177 GLN Y 206 ASN ** Y 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 280 HIS Z 77 ASN Z 114 HIS Z 146 GLN ** Z 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 231 GLN ** Z 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 189 GLN 1 106 HIS 1 366 HIS 2 67 ASN 2 216 ASN 3 189 GLN 4 280 HIS ** 4 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 354 ASN ** 5 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 189 GLN 7 206 ASN 7 343 GLN 8 147 GLN ** 8 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 105 GLN 9 260 GLN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.265 85272 Z= 0.956 Angle : 2.727 50.687 115992 Z= 1.786 Chirality : 0.540 6.393 13164 Planarity : 0.005 0.082 14808 Dihedral : 10.274 178.790 12048 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.04 % Allowed : 29.09 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.08), residues: 10644 helix: 0.46 (0.08), residues: 4248 sheet: 0.24 (0.13), residues: 1416 loop : -0.46 (0.09), residues: 4980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP U 169 HIS 0.021 0.002 HIS Y 70 PHE 0.023 0.002 PHE 2 129 TYR 0.041 0.002 TYR 9 133 ARG 0.010 0.001 ARG I 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2486 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 450 poor density : 2036 time to evaluate : 7.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 450 outliers final: 180 residues processed: 2314 average time/residue: 0.7891 time to fit residues: 3145.5427 Evaluate side-chains 1846 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1666 time to evaluate : 7.127 Switching outliers to nearest non-outliers outliers start: 180 outliers final: 0 residues processed: 180 average time/residue: 0.6341 time to fit residues: 224.4534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 949 optimal weight: 8.9990 chunk 722 optimal weight: 5.9990 chunk 498 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 458 optimal weight: 10.0000 chunk 645 optimal weight: 6.9990 chunk 964 optimal weight: 0.0870 chunk 1020 optimal weight: 0.0070 chunk 503 optimal weight: 10.0000 chunk 913 optimal weight: 0.0000 chunk 275 optimal weight: 0.0020 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN D 60 GLN ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN F 232 GLN F 268 ASN ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN ** G 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN ** H 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 232 GLN J 183 ASN J 206 ASN J 343 GLN ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 173 GLN P 206 ASN Q 147 GLN ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 GLN S 109 HIS S 206 ASN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 GLN W 147 GLN ** W 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 GLN X 232 GLN Y 136 ASN Y 177 GLN Y 205 HIS ** Y 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 ASN ** Z 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 231 GLN ** Z 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 216 ASN ** 3 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 13 GLN 4 136 ASN ** 4 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 81 ASN 7 185 HIS 8 187 ASN 8 188 ASN ** 8 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 260 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.6797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.248 85272 Z= 0.943 Angle : 2.713 50.661 115992 Z= 1.780 Chirality : 0.540 6.513 13164 Planarity : 0.005 0.065 14808 Dihedral : 10.078 179.657 12048 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.20 % Allowed : 30.04 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.08), residues: 10644 helix: 0.52 (0.08), residues: 4176 sheet: 0.05 (0.13), residues: 1416 loop : -0.57 (0.08), residues: 5052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP U 169 HIS 0.017 0.001 HIS D 70 PHE 0.019 0.002 PHE A 365 TYR 0.041 0.002 TYR 9 133 ARG 0.014 0.001 ARG 1 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2273 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 375 poor density : 1898 time to evaluate : 7.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 375 outliers final: 180 residues processed: 2144 average time/residue: 0.7853 time to fit residues: 2906.7683 Evaluate side-chains 1812 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1632 time to evaluate : 7.180 Switching outliers to nearest non-outliers outliers start: 180 outliers final: 0 residues processed: 180 average time/residue: 0.6483 time to fit residues: 229.2433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 850 optimal weight: 5.9990 chunk 579 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 760 optimal weight: 6.9990 chunk 421 optimal weight: 4.9990 chunk 871 optimal weight: 9.9990 chunk 705 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 521 optimal weight: 9.9990 chunk 916 optimal weight: 5.9990 chunk 257 optimal weight: 0.2980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN D 206 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN E 268 GLN G 128 ASN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 GLN I 232 GLN J 13 GLN J 183 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 GLN M 279 GLN M 366 HIS ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN Q 187 ASN Q 216 ASN ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 206 ASN T 67 ASN T 258 GLN ** V 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 147 GLN W 149 GLN ** W 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 GLN Y 104 ASN Y 177 GLN Y 206 ASN ** Y 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 ASN Z 146 GLN ** Z 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 216 ASN ** 1 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 206 ASN 1 280 HIS 1 366 HIS 2 217 GLN ** 3 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 128 ASN 4 136 ASN ** 4 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 194 GLN ** 6 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 183 ASN 7 206 ASN ** 8 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 188 ASN ** 8 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 113 GLN 9 260 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.7671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.249 85272 Z= 0.964 Angle : 2.725 50.705 115992 Z= 1.786 Chirality : 0.540 6.394 13164 Planarity : 0.005 0.068 14808 Dihedral : 9.965 179.033 12048 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.12 % Allowed : 30.56 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.08), residues: 10644 helix: 0.32 (0.08), residues: 4176 sheet: -0.28 (0.13), residues: 1500 loop : -0.76 (0.08), residues: 4968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP U 169 HIS 0.017 0.002 HIS 1 101 PHE 0.031 0.002 PHE P 227 TYR 0.038 0.002 TYR L 133 ARG 0.010 0.001 ARG 7 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2194 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 1826 time to evaluate : 7.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 368 outliers final: 172 residues processed: 2102 average time/residue: 0.7909 time to fit residues: 2850.3471 Evaluate side-chains 1682 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1510 time to evaluate : 7.211 Switching outliers to nearest non-outliers outliers start: 172 outliers final: 0 residues processed: 172 average time/residue: 0.6465 time to fit residues: 216.6237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 343 optimal weight: 9.9990 chunk 919 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 599 optimal weight: 2.9990 chunk 251 optimal weight: 0.7980 chunk 1021 optimal weight: 0.9990 chunk 848 optimal weight: 5.9990 chunk 473 optimal weight: 3.9990 chunk 84 optimal weight: 0.0470 chunk 337 optimal weight: 9.9990 chunk 536 optimal weight: 6.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 206 ASN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN C 58 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN C 260 GLN D 206 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN G 206 ASN G 269 GLN ** G 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN P 136 ASN P 339 ASN P 343 GLN Q 216 ASN ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 245 ASN R 173 GLN ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 206 ASN ** V 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 136 ASN V 185 HIS V 206 ASN W 152 HIS ** W 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 232 GLN Y 104 ASN Y 136 ASN Y 177 GLN Y 206 ASN Y 214 GLN Z 77 ASN ** Z 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 144 GLN ** 1 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 206 ASN 1 269 GLN 2 77 ASN ** 2 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 4 206 ASN ** 4 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 216 ASN ** 6 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 81 ASN 6 260 GLN 7 183 ASN 7 206 ASN 7 269 GLN 7 343 GLN 8 187 ASN ** 8 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.8029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.250 85272 Z= 0.943 Angle : 2.709 50.676 115992 Z= 1.779 Chirality : 0.539 6.408 13164 Planarity : 0.005 0.061 14808 Dihedral : 9.780 179.784 12048 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.97 % Allowed : 31.32 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.08), residues: 10644 helix: 0.35 (0.08), residues: 4272 sheet: -0.23 (0.13), residues: 1464 loop : -0.69 (0.09), residues: 4908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP L 169 HIS 0.012 0.001 HIS D 70 PHE 0.025 0.002 PHE M 227 TYR 0.041 0.002 TYR 9 133 ARG 0.008 0.001 ARG 7 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1972 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1707 time to evaluate : 7.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 265 outliers final: 138 residues processed: 1887 average time/residue: 0.7987 time to fit residues: 2592.9854 Evaluate side-chains 1620 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1482 time to evaluate : 7.251 Switching outliers to nearest non-outliers outliers start: 138 outliers final: 0 residues processed: 138 average time/residue: 0.6709 time to fit residues: 183.2811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 985 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 582 optimal weight: 0.9990 chunk 746 optimal weight: 8.9990 chunk 578 optimal weight: 9.9990 chunk 860 optimal weight: 9.9990 chunk 570 optimal weight: 5.9990 chunk 1017 optimal weight: 0.7980 chunk 636 optimal weight: 0.9990 chunk 620 optimal weight: 4.9990 chunk 469 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN C 58 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN C 260 GLN ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 HIS E 147 GLN G 206 ASN ** G 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 GLN ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 GLN M 136 ASN M 138 GLN M 205 HIS M 206 ASN ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 GLN P 343 GLN ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 109 HIS S 206 ASN S 372 HIS ** V 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 136 ASN V 206 ASN W 149 GLN ** W 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 104 ASN Y 128 ASN Y 177 GLN Y 206 ASN ** Y 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 ASN ** Z 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 216 ASN 1 138 GLN 1 206 ASN 2 77 ASN 4 128 ASN ** 4 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 206 ASN 4 269 GLN ** 4 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 216 ASN ** 6 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 183 ASN ** 8 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 187 ASN ** 8 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.8306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.245 85272 Z= 0.944 Angle : 2.708 50.625 115992 Z= 1.778 Chirality : 0.540 6.396 13164 Planarity : 0.005 0.054 14808 Dihedral : 9.639 179.432 12048 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.16 % Allowed : 31.84 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.08), residues: 10644 helix: 0.36 (0.08), residues: 4284 sheet: -0.22 (0.14), residues: 1392 loop : -0.74 (0.09), residues: 4968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 169 HIS 0.018 0.001 HIS V 101 PHE 0.030 0.002 PHE A 227 TYR 0.035 0.002 TYR L 133 ARG 0.010 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1810 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1617 time to evaluate : 7.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 193 outliers final: 88 residues processed: 1752 average time/residue: 0.8104 time to fit residues: 2438.3408 Evaluate side-chains 1532 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1444 time to evaluate : 7.128 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 0 residues processed: 88 average time/residue: 0.6422 time to fit residues: 116.2038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 629 optimal weight: 0.6980 chunk 406 optimal weight: 0.9990 chunk 607 optimal weight: 9.9990 chunk 306 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 197 optimal weight: 20.0000 chunk 647 optimal weight: 8.9990 chunk 693 optimal weight: 10.0000 chunk 503 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 800 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN B 187 ASN C 58 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN C 232 GLN C 260 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN D 333 HIS ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 GLN J 13 GLN ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN M 206 ASN ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 HIS ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 206 ASN ** W 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 104 ASN Y 128 ASN Y 136 ASN Y 206 ASN ** Y 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 ASN ** Z 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 206 ASN 1 339 ASN ** 3 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 128 ASN 4 136 ASN ** 4 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.8673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.248 85272 Z= 0.956 Angle : 2.715 50.732 115992 Z= 1.782 Chirality : 0.541 6.495 13164 Planarity : 0.005 0.081 14808 Dihedral : 9.612 179.867 12048 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.67 % Allowed : 32.63 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.08), residues: 10644 helix: 0.39 (0.08), residues: 4152 sheet: -0.34 (0.13), residues: 1548 loop : -0.82 (0.09), residues: 4944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 169 HIS 0.017 0.001 HIS V 101 PHE 0.034 0.002 PHE P 227 TYR 0.036 0.002 TYR X 133 ARG 0.011 0.001 ARG 4 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1710 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1561 time to evaluate : 7.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 87 residues processed: 1658 average time/residue: 0.8063 time to fit residues: 2288.6786 Evaluate side-chains 1505 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1418 time to evaluate : 7.240 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.6642 time to fit residues: 117.7095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 925 optimal weight: 7.9990 chunk 975 optimal weight: 6.9990 chunk 889 optimal weight: 1.9990 chunk 948 optimal weight: 8.9990 chunk 974 optimal weight: 2.9990 chunk 570 optimal weight: 7.9990 chunk 413 optimal weight: 6.9990 chunk 744 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 chunk 857 optimal weight: 3.9990 chunk 897 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN C 260 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN G 206 ASN ** G 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 GLN ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN P 136 ASN P 343 GLN ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 113 GLN V 206 ASN ** W 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 128 ASN Y 206 ASN ** Y 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 ASN ** Z 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 216 ASN ** 1 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 339 ASN ** 3 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 58 GLN 4 128 ASN 4 136 ASN ** 4 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 147 GLN ** 6 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 185 HIS ** 8 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.9022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.246 85272 Z= 0.974 Angle : 2.725 50.752 115992 Z= 1.786 Chirality : 0.541 6.429 13164 Planarity : 0.005 0.060 14808 Dihedral : 9.704 179.722 12048 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.21 % Allowed : 33.21 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.08), residues: 10644 helix: 0.25 (0.08), residues: 4176 sheet: -0.54 (0.13), residues: 1512 loop : -0.90 (0.09), residues: 4956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 169 HIS 0.021 0.001 HIS P 101 PHE 0.030 0.002 PHE P 227 TYR 0.035 0.002 TYR 3 133 ARG 0.009 0.001 ARG 4 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1589 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1481 time to evaluate : 7.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 62 residues processed: 1546 average time/residue: 0.8275 time to fit residues: 2183.0919 Evaluate side-chains 1426 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1364 time to evaluate : 7.312 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.6774 time to fit residues: 87.3138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 945 optimal weight: 4.9990 chunk 622 optimal weight: 0.9980 chunk 1002 optimal weight: 0.5980 chunk 612 optimal weight: 6.9990 chunk 475 optimal weight: 0.4980 chunk 697 optimal weight: 6.9990 chunk 1052 optimal weight: 5.9990 chunk 968 optimal weight: 20.0000 chunk 837 optimal weight: 8.9990 chunk 86 optimal weight: 0.0670 chunk 647 optimal weight: 5.9990 overall best weight: 1.4320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN C 58 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN F 24 GLN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN H 77 ASN ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 343 GLN ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 GLN ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 138 GLN V 206 ASN ** W 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 136 ASN Y 206 ASN ** Y 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 ASN ** Z 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 216 ASN ** 1 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 206 ASN 2 77 ASN 2 147 GLN 3 58 GLN ** 4 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 128 ASN 4 136 ASN ** 4 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 85 GLN ** 6 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 206 ASN ** 8 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.9169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.247 85272 Z= 0.945 Angle : 2.713 50.620 115992 Z= 1.780 Chirality : 0.539 6.368 13164 Planarity : 0.005 0.052 14808 Dihedral : 9.550 179.868 12048 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.52 % Allowed : 33.61 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.08), residues: 10644 helix: 0.35 (0.08), residues: 4224 sheet: -0.59 (0.13), residues: 1476 loop : -0.78 (0.09), residues: 4944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP O 169 HIS 0.018 0.001 HIS P 101 PHE 0.027 0.002 PHE P 227 TYR 0.042 0.002 TYR L 133 ARG 0.010 0.001 ARG H 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21288 Ramachandran restraints generated. 10644 Oldfield, 0 Emsley, 10644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1555 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1509 time to evaluate : 7.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 22 residues processed: 1539 average time/residue: 0.8447 time to fit residues: 2213.5568 Evaluate side-chains 1407 residues out of total 8928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1385 time to evaluate : 7.343 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.7566 time to fit residues: 39.9748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 513 optimal weight: 8.9990 chunk 665 optimal weight: 1.9990 chunk 892 optimal weight: 0.9990 chunk 256 optimal weight: 2.9990 chunk 772 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 232 optimal weight: 8.9990 chunk 839 optimal weight: 5.9990 chunk 351 optimal weight: 10.0000 chunk 861 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN C 58 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN D 206 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN ** G 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN ** N 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 343 GLN ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 GLN ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 GLN S 138 GLN V 13 GLN V 138 GLN ** W 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 58 GLN ** Y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 138 GLN Y 206 ASN ** Y 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 339 ASN Z 77 ASN ** Z 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 339 ASN 4 128 ASN 4 136 ASN ** 4 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105000 restraints weight = 102470.720| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.05 r_work: 0.3119 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.9298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.244 85272 Z= 0.944 Angle : 2.711 50.604 115992 Z= 1.780 Chirality : 0.539 6.351 13164 Planarity : 0.005 0.052 14808 Dihedral : 9.428 179.704 12048 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.64 % Allowed : 34.13 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.08), residues: 10644 helix: 0.48 (0.08), residues: 4152 sheet: -0.61 (0.13), residues: 1476 loop : -0.71 (0.09), residues: 5016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP X 169 HIS 0.017 0.001 HIS P 101 PHE 0.036 0.002 PHE S 227 TYR 0.031 0.002 TYR U 133 ARG 0.009 0.001 ARG J 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41670.57 seconds wall clock time: 721 minutes 44.70 seconds (43304.70 seconds total)